Diff of the two buildlogs: -- --- b1/build.log 2024-05-10 18:49:26.125703635 +0000 +++ b2/build.log 2024-05-10 18:58:15.731140206 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 10 06:32:55 -12 2024 -I: pbuilder-time-stamp: 1715365975 +I: Current time: Fri Jun 13 15:12:31 +14 2025 +I: pbuilder-time-stamp: 1749777151 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -46,52 +46,84 @@ dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3053116/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jun 13 01:12 /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/310429/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3ba01d05136142559eef055b11e2f977' - 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='3053116' - PS1='# ' - PS2='> ' + INVOCATION_ID=57e2492630ee44e6a8d4dbd55283077b + 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=310429 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.dfmi9fcw/pbuilderrc_TBXa --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.dfmi9fcw/b1 --logfile b1/build.log spades_3.15.5+dfsg-7.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://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dfmi9fcw/pbuilderrc_lPfp --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.dfmi9fcw/b2 --logfile b2/build.log spades_3.15.5+dfsg-7.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3053116/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 11 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -331,7 +363,7 @@ Get: 156 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-joblib all 1.3.2-2 [218 kB] -Fetched 203 MB in 17s (12.2 MB/s) +Fetched 203 MB in 3s (62.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -850,8 +882,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri May 10 18:34:44 UTC 2024. -Universal Time is now: Fri May 10 18:34:44 UTC 2024. +Local time is now: Fri Jun 13 01:13:45 UTC 2025. +Universal Time is now: Fri Jun 13 01:13:45 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -999,7 +1031,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-7_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.5+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -1262,8 +1298,8 @@ CMake that the project does not need compatibility with older versions. --- Configuring done (18.3s) --- Generating done (0.4s) +-- Configuring done (8.2s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -1277,7 +1313,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_build -- all debruijn_test include_test - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1295,32 +1331,32 @@ make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend -make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake "--color=" +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gfa1 /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend +make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" -make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -1335,90 +1371,134 @@ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory 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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-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.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 -[ 2%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -[ 1%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -[ 1%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.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/Mutation.cpp.o +[ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.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 +[ 1%] Building CXX object 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CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp +[ 6%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o +[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o +[ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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-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-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp +[ 6%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_MALLOC_OVERRIDE_GLIBC -DMI_SHOW_ERRORS=1 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CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/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-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp -[ 2%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/version.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/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-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp +[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o cd 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projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -MF CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o.d -o CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp +[ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem 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-DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/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-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp +[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o +[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:610:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 610 | printf("%02llx ", j); @@ -1467,10 +1547,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1615:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1615 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Linking CXX static library libversion.a +[ 8%] Linking CXX static library libversion.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 /usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o +[ 8%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp +[ 8%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp +/usr/bin/ranlib libversion.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:466:15: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'mem_region_t' {aka 'struct mem_region_s'} with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] @@ -1489,7 +1574,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ -/usr/bin/ranlib libversion.a In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc.c:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c: At global scope: @@ -1592,6 +1676,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] @@ -1600,91 +1685,170 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 3%] Built target version -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp -[ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -MF CMakeFiles/ConsensusCore.dir/Version.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Version.cpp -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o +[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp +[ 9%] Built target version +[ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp +[ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_alphabet.c -[ 5%] Linking C static library libgqf.a +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp +[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp +[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp +[ 11%] Linking C static library libgqf.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P 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CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp -[ 5%] Linking CXX static library libgetopt_pp.a +[ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o +[ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o +[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp +[ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp +[ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp +[ 16%] Linking CXX static library libgetopt_pp.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -[ 5%] Linking C static library libgfa1.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake +[ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp /usr/bin/ranlib libgetopt_pp.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 -/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-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c -[ 5%] Built target getopt_pp +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o +[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp +[ 18%] Linking CXX static library libedlib.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +[ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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/usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] + 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { + | ^~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? + | ^~~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 6%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp -[ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp -[ 8%] Linking CXX static library libedlib.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +[ 19%] Linking C static library libgfa1.a +[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 -/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o -/usr/bin/ranlib libedlib.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 8%] Built target edlib +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 +/usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' + 578 | _bgzf_read(fp->fp, buf, 28); + | ^~~~~~~~~~ +[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o +[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o +[ 20%] Built target edlib make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] - 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { - | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? - | ^~~~~~~ -[ 9%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c +[ 23%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp -[ 9%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/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-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -1706,11 +1870,22 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] @@ -1722,256 +1897,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] -[ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp -[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp -[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp -[ 10%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp -[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp -[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c -[ 10%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp -[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c -[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c -[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp -[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/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-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp -[ 12%] Linking CXX static library libsequence.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 -/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o -[ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c -/usr/bin/ranlib libsequence.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 12%] Built target sequence -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp -[ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] - 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); - | ^~~ -[ 15%] Linking CXX static library libformat.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c -[ 15%] Built target mimalloc-obj -[ 15%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp -/usr/bin/ranlib libformat.a -[ 15%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/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-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 15%] Built target format -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 15%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/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-3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp -[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c -[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp -[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -[ 15%] Linking CXX static library libcoverage_model.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 -/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -/usr/bin/ranlib libcoverage_model.a -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp -[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 16%] Built target coverage_model -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp -[ 16%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] - 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? - 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] - 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? - 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; - | ^ -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp -[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c -[ 18%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/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-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp -[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c -[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c -[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' - 578 | _bgzf_read(fp->fp, buf, 28); - | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1987,42 +1915,49 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ -[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] + 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? + 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] + 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? + 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; + | ^ +/usr/bin/ranlib libgfa1.a +[ 23%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp +[ 24%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c -[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c -[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 24%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c +[ 24%] Built target gfa1 +[ 24%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] 344 | fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", @@ -2042,6 +1977,8 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ +[ 25%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); @@ -2053,42 +1990,19 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c -[ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 25%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp +[ 25%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c +[ 25%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined @@ -2101,33 +2015,37 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ -[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o +[ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp +[ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o +[ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] + 94 | mi = ::mallinfo(); + | ~~~~~~~~~~^~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: +/usr/include/malloc.h:114:24: note: declared here + 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; + | ^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -2142,8 +2060,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -2158,272 +2074,267 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp -[ 23%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp -[ 24%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c +[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o +[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c +[ 30%] Linking CXX static library libsequence.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 +/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp +/usr/bin/ranlib libsequence.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/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-3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp +[ 31%] Built target sequence +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c -[ 24%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c -[ 24%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp -[ 24%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c -[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, - from /usr/include/c++/13/bits/allocator.h:46, - from /usr/include/c++/13/vector:63, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/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))); - | ^ -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/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))); - | ^ -[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp -[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o +[ 32%] Linking CXX static library libformat.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 +/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp +/usr/bin/ranlib libformat.a +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 32%] Built target format +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_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-3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o cd 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ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o +[ 32%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/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-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c -[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp -[ 27%] Linking CXX static library libmapping_printer.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +[ 33%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c +[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 -/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -/usr/bin/ranlib libmapping_printer.a -[ 29%] Linking CXX static library libBamTools.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +[ 33%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c +[ 34%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 -[ 29%] Built target mapping_printer -/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 -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp -[ 29%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/JSON.cpp -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp -/usr/bin/ranlib libBamTools.a +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] + 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); + | ^~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp -[ 30%] Built target BamTools -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o +[ 34%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +[ 34%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c +[ 36%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/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-3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp +[ 36%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp +[ 36%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp +[ 37%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c +[ 37%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c +[ 37%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c -[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm 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-/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c +[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_random.c +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 +[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o +cd 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 36%] Linking CXX static library libgraphio.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 -/usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] - 94 | mi = ::mallinfo(); - | ~~~~~~~~~~^~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: -/usr/include/malloc.h:114:24: note: declared here - 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; - | ^~~~~~~~ -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c +/usr/bin/ranlib libBamTools.a +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +[ 41%] Building C object 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ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c +[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c +[ 43%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c +[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kstring.c -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c -[ 37%] Built target graphio -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp -[ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_aux.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c -[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2433,7 +2344,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ -[ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ @@ -2443,52 +2353,49 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c -[ 38%] Linking CXX static library libutils.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c -/usr/bin/ranlib libutils.a +[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp -[ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c -[ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c -[ 40%] Built target utils -[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c -[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam.c -[ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c -[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd 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CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:178:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; @@ -2518,37 +2425,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -cd 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ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp -[ 43%] Linking CXX static library libpaired_info.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 -/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -[ 44%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -cd 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ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c -[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem 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ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_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-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c +[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bedidx.c +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); @@ -2590,61 +2478,17 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c -[ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include 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ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_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-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c -[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_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-3.15.5+dfsg/assembler/ext/src/samtools/sam_header.c -[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c -[ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS 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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-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c -[ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp -[ 47%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c -[ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp -[ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c -[ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c -[ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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[-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o CMakeFiles/easel.dir/esl_getopts.c.o CMakeFiles/easel.dir/esl_gev.c.o CMakeFiles/easel.dir/esl_gumbel.c.o CMakeFiles/easel.dir/esl_heap.c.o CMakeFiles/easel.dir/esl_histogram.c.o 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function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2680,7 +2539,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/usr/bin/ranlib libeasel.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 50%] Built target easel make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend @@ -2689,66 +2547,136 @@ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -[ 50%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxb.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxchk.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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61%] Built target samtools +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c +[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/decoding.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, + from /usr/include/c++/13/bits/allocator.h:46, + from /usr/include/c++/13/vector:63, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/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 libutils.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 +/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" +/usr/bin/ranlib libutils.a +[ 65%] Linking CXX static library libmapping_printer.a +cd 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +[ 68%] Linking C static library libhmmer.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o 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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-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target hmmer +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +[ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp +[ 68%] Linking CXX static library libpaired_info.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 +/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o +/usr/bin/ranlib libpaired_info.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target paired_info +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': +/usr/include/c++/13/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:163:21: required from 'void utils::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:43:21: required from 'void utils::PerfectHashMapBuilder::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:144:39: required from 'void utils::BuildIndex(PerfectHashMap&, const KMerStorage&, size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:249:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:27:39: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:31:64: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' + 20 | IdHolder edge_id_; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 161 | pli->Z = pli->domZ = cfg.Z; + | ~~~~^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 68%] Linking CXX static library libhmmercpp.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +/usr/bin/ranlib libhmmercpp.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target hmmercpp +[ 68%] Linking CXX static library ../../../lib/libgtest.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/usr/bin/ranlib ../../../lib/libgtest.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 68%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o +[ 68%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +[ 68%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -2796,29 +3039,15 @@ /usr/include/c++/13/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))); | ^ -[ 56%] Built target samtools -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -cd 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmm.c +[ 68%] Linking CXX static library libConsensusCore.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 +/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o +[ 68%] Linking CXX static library ../../../lib/libgtest_main.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +/usr/bin/ranlib ../../../lib/libgtest_main.a In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -2841,30 +3070,14 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_scoredata.c -[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_trace.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_tophits.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -MF CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o.d -o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmpgmd2msa.c +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +/usr/bin/ranlib libConsensusCore.a +[ 68%] Built target gtest_main +[ 68%] Linking CXX static library libteamcity_gtest.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +/usr/bin/ranlib libteamcity_gtest.a In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] @@ -2887,208 +3100,76 @@ /usr/include/c++/13/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))); | ^ -[ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -MF CMakeFiles/hmmer.dir/src/fm_alphabet.c.o.d -o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_alphabet.c -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_general.c -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/decoding.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -[ 63%] Linking CXX static library ../../../lib/libgtest.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/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))); - | ^ -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c -[ 65%] Linking CXX static library libConsensusCore.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 -/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -/usr/bin/ranlib ../../../lib/libgtest.a -/usr/bin/ranlib libConsensusCore.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target gtest -make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp -[ 65%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -[ 65%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem 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ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc -[ 65%] Linking CXX static library libllvm-support.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 -/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Built target ConsensusCore +[ 68%] Built target teamcity_gtest +[ 68%] Built target ConsensusCore make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -[ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -[ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o +[ 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/gap_closer.cpp.o +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.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/contig_output_stage.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp +[ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp -[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp -/usr/bin/ranlib libllvm-support.a -[ 68%] Linking CXX static library ../../../lib/libgtest_main.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -/usr/bin/ranlib ../../../lib/libgtest_main.a -[ 68%] Linking CXX static library libteamcity_gtest.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target gtest_main -/usr/bin/ranlib libteamcity_gtest.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target teamcity_gtest -[ 68%] Built target llvm-support -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp -[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp -[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); | ^~~~ -[ 69%] Linking CXX static library libbinary_io.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 -/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o -[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp -/usr/bin/ranlib libbinary_io.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp -[ 69%] Built target binary_io -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 216 | for (;index != res.first; ++index) { - | ~~~~~~^~~~~~~~~~~~ -[ 69%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 243 | if (coords.second + 5000 > path.Length()) { - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, long unsigned int>]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:103:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:230:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:102:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:93:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:165:31: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] - 28 | size_t min_dist, - | ~~~~~~~^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 235 | if (data.median_insert_size < gp.k() + 2) @@ -3101,31 +3182,44 @@ /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, long unsigned int>]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:103:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:230:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:102:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:93:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:165:31: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] + 28 | size_t min_dist, + | ~~~~~~~^~~~~~~~ /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ -[ 69%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp -[ 69%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp -[ 70%] Linking C static library libhmmer.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o 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CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp -/usr/bin/ranlib libhmmer.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target hmmer -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" +[ 72%] Linking CXX static library libassembly_graph.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +/usr/bin/ranlib libassembly_graph.a +[ 72%] Linking CXX static library libbinary_io.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 +/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o +/usr/bin/ranlib libbinary_io.a +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -3138,25 +3232,104 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ +[ 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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/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-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 72%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o +[ 73%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o +[ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o +[ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o 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CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp +[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp +[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o +[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o +[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp +[ 77%] 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/connection_condition2015.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o +[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o +cd 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common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 216 | for (;index != res.first; ++index) { + | ~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 243 | if (coords.second + 5000 > path.Length()) { + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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]': + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3181,19 +3354,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3201,6 +3361,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' @@ -3211,24 +3383,6 @@ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, @@ -3241,14 +3395,11 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 161 | pli->Z = pli->domZ = cfg.Z; - | ~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3263,23 +3414,23 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX static library libhmmercpp.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -/usr/bin/ranlib libhmmercpp.a +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 111 | if (iter->second < min_read_count_) { + | ^~~~~~~~~~~~~~~ +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 277 | if (bad_mapping_pos == -1) + | ~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3287,10 +3438,28 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 72%] Built target hmmercpp -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 29 | if (sum < absolute_weight_threshold_) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +[ 80%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp +[ 81%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -3312,29 +3481,22 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp -[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] @@ -3354,11 +3516,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] @@ -3378,6 +3538,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3396,22 +3557,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3419,30 +3564,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3499,25 +3632,34 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3531,6 +3673,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3549,6 +3692,22 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3573,55 +3732,81 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': -/usr/include/c++/13/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:163:21: required from 'void utils::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:43:21: required from 'void utils::PerfectHashMapBuilder::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:144:39: required from 'void utils::BuildIndex(PerfectHashMap&, const KMerStorage&, size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:249:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:27:39: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:31:64: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' - 20 | IdHolder edge_id_; - | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3634,6 +3819,13 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3652,6 +3844,153 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:34:13: note: in expansion of macro 'SET_PRIORITY' + 34 | SET_PRIORITY(LibraryType::SangerReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' + 35 | SET_PRIORITY(LibraryType::PacBioReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' + 35 | SET_PRIORITY(LibraryType::PacBioReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' + 36 | SET_PRIORITY(LibraryType::NanoporeReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' + 36 | SET_PRIORITY(LibraryType::NanoporeReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' + 37 | SET_PRIORITY(LibraryType::TrustedContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' + 37 | SET_PRIORITY(LibraryType::TrustedContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' + 38 | SET_PRIORITY(LibraryType::SingleReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' + 38 | SET_PRIORITY(LibraryType::SingleReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' + 39 | SET_PRIORITY(LibraryType::PairedEnd); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' + 39 | SET_PRIORITY(LibraryType::PairedEnd); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' + 40 | SET_PRIORITY(LibraryType::HQMatePairs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' + 40 | SET_PRIORITY(LibraryType::HQMatePairs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' + 41 | SET_PRIORITY(LibraryType::MatePairs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' + 41 | SET_PRIORITY(LibraryType::MatePairs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' + 42 | SET_PRIORITY(LibraryType::TSLReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' + 42 | SET_PRIORITY(LibraryType::TSLReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' + 43 | SET_PRIORITY(LibraryType::PathExtendContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' + 43 | SET_PRIORITY(LibraryType::PathExtendContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' + 44 | SET_PRIORITY(LibraryType::UntrustedContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' + 44 | SET_PRIORITY(LibraryType::UntrustedContigs); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' + 45 | SET_PRIORITY(LibraryType::FLRNAReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' + 45 | SET_PRIORITY(LibraryType::FLRNAReads); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here + 28 | #define SET_PRIORITY(o) case o: --priority + | ^~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' + 46 | SET_PRIORITY(LibraryType::AssemblyGraph); + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3717,44 +4056,6 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -3793,6 +4094,59 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] + 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -3815,13 +4169,102 @@ /usr/include/c++/13/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))); | ^ -[ 74%] Linking CXX static library libinput.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 -/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o -/usr/bin/ranlib libinput.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 74%] Built target input +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, @@ -3856,78 +4299,36 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ -[ 74%] Linking CXX static library libassembly_graph.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 -/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -/usr/bin/ranlib libassembly_graph.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 74%] Built target assembly_graph -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +[ 81%] Linking CXX static library libinput.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 +/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o +/usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -[ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp -[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 277 | if (bad_mapping_pos == -1) - | ~~~~~~~~~~~~~~~~^~~~~ -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +[ 81%] Built target input /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3946,80 +4347,25 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp -[ 79%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4038,42 +4384,35 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4092,8 +4431,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4123,16 +4460,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4140,56 +4467,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 29 | if (sum < absolute_weight_threshold_) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] - 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, - from /usr/include/c++/13/bits/allocator.h:46, - from /usr/include/c++/13/bits/alloc_traits.h:39, - from /usr/include/c++/13/ext/alloc_traits.h:34, - from /usr/include/c++/13/bits/hashtable_policy.h:39, - from /usr/include/c++/13/bits/hashtable.h:35, - from /usr/include/c++/13/bits/unordered_map.h:33, - from /usr/include/c++/13/unordered_map:41, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -[ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4202,26 +4479,19 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 111 | if (iter->second < min_read_count_) { - | ^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4235,153 +4505,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:34:13: note: in expansion of macro 'SET_PRIORITY' - 34 | SET_PRIORITY(LibraryType::SangerReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' - 35 | SET_PRIORITY(LibraryType::PacBioReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' - 35 | SET_PRIORITY(LibraryType::PacBioReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' - 36 | SET_PRIORITY(LibraryType::NanoporeReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' - 36 | SET_PRIORITY(LibraryType::NanoporeReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' - 37 | SET_PRIORITY(LibraryType::TrustedContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' - 37 | SET_PRIORITY(LibraryType::TrustedContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' - 38 | SET_PRIORITY(LibraryType::SingleReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' - 38 | SET_PRIORITY(LibraryType::SingleReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' - 39 | SET_PRIORITY(LibraryType::PairedEnd); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' - 39 | SET_PRIORITY(LibraryType::PairedEnd); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' - 40 | SET_PRIORITY(LibraryType::HQMatePairs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' - 40 | SET_PRIORITY(LibraryType::HQMatePairs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' - 41 | SET_PRIORITY(LibraryType::MatePairs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' - 41 | SET_PRIORITY(LibraryType::MatePairs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' - 42 | SET_PRIORITY(LibraryType::TSLReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' - 42 | SET_PRIORITY(LibraryType::TSLReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' - 43 | SET_PRIORITY(LibraryType::PathExtendContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' - 43 | SET_PRIORITY(LibraryType::PathExtendContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' - 44 | SET_PRIORITY(LibraryType::UntrustedContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' - 44 | SET_PRIORITY(LibraryType::UntrustedContigs); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' - 45 | SET_PRIORITY(LibraryType::FLRNAReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' - 45 | SET_PRIORITY(LibraryType::FLRNAReads); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here - 28 | #define SET_PRIORITY(o) case o: --priority - | ^~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' - 46 | SET_PRIORITY(LibraryType::AssemblyGraph); - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4394,12 +4517,83 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, + from /usr/include/c++/13/bits/allocator.h:46, + from /usr/include/c++/13/bits/alloc_traits.h:39, + from /usr/include/c++/13/ext/alloc_traits.h:34, + from /usr/include/c++/13/bits/hashtable_policy.h:39, + from /usr/include/c++/13/bits/hashtable.h:35, + from /usr/include/c++/13/bits/unordered_map.h:33, + from /usr/include/c++/13/unordered_map:41, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h: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=] @@ -4444,22 +4638,19 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4473,6 +4664,25 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -4516,12 +4726,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -4574,29 +4778,59 @@ /usr/include/c++/13/bits/stl_algo.h:1822:17: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__val + offsetof(omnigraph::value_type, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 1822 | __val = _GLIBCXX_MOVE(*__i); | ^~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, + from /usr/include/c++/13/bits/allocator.h:46, + from /usr/include/c++/13/string:43, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4626,47 +4860,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'std::__atomic_base<_IntTp>::__int_type std::__atomic_base<_IntTp>::fetch_add(__int_type, std::memory_order) [with _ITp = int]', inlined from 'void llvm::ThreadSafeRefCountedBase::Retain() const [with Derived = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:94:43, inlined from 'static void llvm::IntrusiveRefCntPtrInfo::retain(T*) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:125:43, @@ -4742,72 +4935,13 @@ /usr/include/c++/13/bits/stl_heap.h:262:18: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__value + offsetof(omnigraph::_ValueType, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 262 | _ValueType __value = _GLIBCXX_MOVE(*__result); | ^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ +[ 81%] Linking CXX static library libmodules.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 +/usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o +/usr/bin/ranlib libmodules.a +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 81%] Built target modules /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4827,6 +4961,10 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 81%] Linking CXX static library libpath_extend.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 +/usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:12: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', @@ -4879,115 +5017,6 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, - from /usr/include/c++/13/bits/allocator.h:46, - from /usr/include/c++/13/string:43, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 81%] Linking CXX static library libspades-stages.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 -/usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" -[ 81%] Linking CXX static library libmodules.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 -/usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -/usr/bin/ranlib libmodules.a -/usr/bin/ranlib libspades-stages.a -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target modules -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target spades-stages -[ 81%] Linking CXX static library libpath_extend.a -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 -/usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target path_extend @@ -4997,15 +5026,15 @@ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+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-3.15.5+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 -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: @@ -5039,75 +5068,82 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 82%] Linking CXX static library libspades-stages.a +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 +/usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] + 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ~~~~~~~^~~~~~~~ +/usr/bin/ranlib libspades-stages.a +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] - 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ~~~~~~~^~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 82%] Built target spades-stages /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5212,55 +5248,55 @@ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend +make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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-Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp +[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem 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CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp +[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.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/BaseHypothesisEvaluator.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp -[ 86%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 85 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); @@ -5312,6 +5348,17 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/HSeq.hpp:93:36: warning: unused parameter 'size' [-Wunused-parameter] 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:357:110: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -5326,17 +5373,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:12: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:357:110: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] 90 | } @@ -5370,21 +5406,6 @@ /build/reproducible-path/spades-3.15.5+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::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:345:28: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:83:52: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -5403,6 +5424,21 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:83:52: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -5697,156 +5733,179 @@ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target common_modules make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend 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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" make -f projects/kmercount/CMakeFiles/spades-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-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" +make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake "--color=" +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" +make -f projects/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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" +make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend -make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend +make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" -make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/spaligner.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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" +make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" -make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build +make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build +make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/main.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build -[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/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-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/main.cpp +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp -[ 87%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp +make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build -[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp -make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp +make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 89%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp -[ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp -make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 89%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_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-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp -[ 89%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -[ 89%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -[ 90%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -[ 91%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -[ 91%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o +[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +[ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +[ 88%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +[ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o +[ 88%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o +[ 88%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +[ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o +[ 89%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o +[ 91%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp +[ 91%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp +[ 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-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/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-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp +[ 91%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o +[ 91%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp +[ 93%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter 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projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o +[ 94%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp +[ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o +[ 94%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer 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CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/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-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/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-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/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-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] - 135 | pipeline_type mode = cfg::get().mode; - | ^~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ +[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o +[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o +[ 95%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o +[ 95%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem 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-I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { @@ -5854,6 +5913,32 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; + | ~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] + 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { + | ~~~~~~~^~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] + 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { + | ~~~~^~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 357 | for (uint32_t j=0; j, std::allocator >&, size_t)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 275 | for (EdgeId e : annotated) { + | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 465 | for (EdgeId e : annotated) { + | ^ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] + 103 | const bool using_edge_qual = edge_qual.IsAttached(); + | ^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] @@ -5886,26 +6031,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp -[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] @@ -5927,7 +6055,7 @@ | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] @@ -5947,22 +6075,18 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] @@ -5972,10 +6096,18 @@ 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5983,11 +6115,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5995,7 +6140,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] @@ -6007,7 +6152,31 @@ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -6015,10 +6184,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': @@ -6048,30 +6213,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 94%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/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-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 95%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp +[ 96%] Linking CXX executable ../../bin/spades-core +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/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 In file included from /usr/include/string.h:548, from /usr/include/c++/13/cstring:42, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, @@ -6187,58 +6331,29 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 40 into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] - 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { - | ~~~~~~~^~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] - 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { - | ~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] - 103 | const bool using_edge_qual = edge_qual.IsAttached(); - | ^~~~~~~~~~~~~~~ -[ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp -[ 96%] Linking CXX executable ../../bin/spades-core -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm -[ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp -[ 96%] Linking CXX executable ../../bin/spades-truseq-scfcorrection -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 357 | for (uint32_t j=0; j::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Linking CXX executable ../../bin/spades-corrector-core +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-corrector-core -[ 96%] Built target spades-kmer-estimating -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; - | ~~~~~~~~~~^~~~~~~~~~~ +[ 96%] Linking CXX executable ../../bin/spades-truseq-scfcorrection +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-core +[ 96%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-truseq-scfcorrection +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-convert-bin-to-fasta +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable ../../bin/spades-hammer +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-hammer /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6359,28 +6485,39 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] - 248 | EdgeSet ProcessComponent(const VertexSet &reached, - | ~~~~~~~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 275 | for (EdgeId e : annotated) { - | ^ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 465 | for (EdgeId e : annotated) { - | ^ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable ../../bin/spades-kmer-estimating +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 97%] Built target spades-kmer-estimating /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6437,73 +6574,20 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 97%] Linking CXX executable ../../bin/spades-read-filter +[ 97%] Linking CXX executable ../../bin/spades-kmercount +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Built target spades-kmercount /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable ../../bin/unitig-coverage -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6516,7 +6600,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -6527,8 +6610,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-read-filter +[ 98%] Linking CXX executable ../../bin/spades-gmapper +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6547,6 +6631,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -6557,30 +6642,29 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ +[ 98%] Built target spades-read-filter make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 97%] Built target unitig-coverage -[ 97%] Linking CXX executable ../../bin/spades-kmercount -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -[ 97%] Linking CXX executable ../../bin/form_truealignments +[ 98%] Built target spades-gmapper +[ 98%] Linking CXX executable ../../bin/unitig-coverage +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Linking CXX executable ../../bin/spaligner +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Linking CXX executable ../../bin/form_truealignments cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-kmercount +[ 98%] Built target unitig-coverage +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target form_truealignments +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spaligner +[100%] Linking CXX executable ../../bin/cds-subgraphs +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target form_truealignments +[100%] Built target cds-subgraphs /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6599,35 +6683,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable ../../bin/spades-gmapper -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -[ 97%] Linking CXX executable ../../bin/spaligner -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-gmapper -[ 97%] Built target spaligner -[ 98%] Linking CXX executable ../../bin/spades-hammer -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-hammer -[ 98%] Linking CXX executable ../../bin/cds-mapping-stats -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target cds-mapping-stats /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6646,6 +6701,9 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX executable ../../bin/cds-mapping-stats +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -6656,44 +6714,17 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/spades-gbuilder -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-gbuilder -[100%] Linking CXX executable ../../bin/cds-subgraphs -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target cds-subgraphs -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target cds-mapping-stats /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6722,6 +6753,11 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ +[100%] Linking CXX executable ../../bin/spades-gbuilder +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[100%] Built target spades-gbuilder [100%] Linking CXX executable ../../bin/mag-improve cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/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/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so @@ -6744,10 +6780,10 @@ 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[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" +make -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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend @@ -6756,230 +6792,253 @@ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory 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Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". +Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". 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Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +[ 2%] Built target version +[ 7%] Built target gqf +[ 7%] Built target mimalloc-obj +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 11%] Built target edlib +[ 11%] Built target format +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +[ 11%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +[ 11%] Built target binary_io +[ 11%] Built target coverage_model +[ 11%] Built target paired_info Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". +Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". +Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". +Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file 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"/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". +Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target sequence -Consolidate compiler generated dependencies of target version -Consolidate compiler generated dependencies of target gqf -Consolidate compiler generated dependencies of target coverage_model -Consolidate compiler generated dependencies of target binary_io -Consolidate compiler generated dependencies of target paired_info -Consolidate compiler generated dependencies of target format -Consolidate compiler generated dependencies of target mimalloc-obj +Consolidate compiler generated dependencies of target teamcity_gtest +Consolidate compiler generated dependencies of target utils Consolidate compiler generated dependencies of target BamTools +Consolidate compiler generated dependencies of target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory 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ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.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-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target llvm-support -[ 9%] Built target gqf +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Built target version -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -[ 11%] Built target mimalloc-obj -[ 11%] Built target gtest -[ 11%] Built target binary_io -[ 11%] Built target paired_info -[ 21%] Built target sequence -[ 19%] Built target format +[ 11%] Built target teamcity_gtest +[ 14%] Built target sequence [ 33%] Built target BamTools -[ 11%] Built target coverage_model 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[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" +[ 35%] Built target utils +[ 57%] Built target llvm-support +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". @@ -6988,45 +7047,22 @@ Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -[ 54%] Built target llvm-support -Consolidate compiler generated dependencies of target teamcity_gtest -Consolidate compiler generated dependencies of target utils -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 54%] Built target teamcity_gtest -[ 57%] Built target utils -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +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-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target samtools make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -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-3.15.5+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-3.15.5+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-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -[ 64%] Built target samtools +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +[ 64%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" @@ -7040,58 +7076,65 @@ Dependencies file "common/io/CMakeFiles/input.dir/sam/read.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.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-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build 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-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 69%] Built target assembly_graph -Consolidate compiler generated dependencies of target input -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 73%] Built target input make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -[ 73%] Built target input +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". 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Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". -Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target modules +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build +[ 78%] Built target modules make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 83%] Built target path_extend +[ 88%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" @@ -7100,13 +7143,6 @@ Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target modules -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 88%] Built target modules Consolidate compiler generated dependencies of target pipeline make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build @@ -7146,29 +7182,29 @@ make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 92%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -MF CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.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/graph_alignment_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_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-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test.cpp @@ -7202,6 +7238,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:46:38: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': @@ -7222,24 +7276,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:46:38: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 104 | gap_cfg.penalty_ratio = 0.1; + | ^~~ +/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': +/build/reproducible-path/spades-3.15.5+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){ + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 183 | if (g.int_id(*it) == eid_int){ + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 191 | gap_cfg.penalty_ratio = 0.1; + | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here @@ -7255,6 +7309,36 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -7278,40 +7362,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 104 | gap_cfg.penalty_ratio = 0.1; - | ^~~ -/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': -/build/reproducible-path/spades-3.15.5+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){ - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 183 | if (g.int_id(*it) == eid_int){ - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 191 | gap_cfg.penalty_ratio = 0.1; - | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -7324,14 +7374,12 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ @@ -7339,6 +7387,30 @@ 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/reproducible-path/spades-3.15.5+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]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] @@ -7375,67 +7447,45 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/reproducible-path/spades-3.15.5+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]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/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-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7464,48 +7514,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': @@ -7547,6 +7555,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' @@ -7554,6 +7580,16 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/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-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' @@ -7572,6 +7608,24 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' @@ -7591,6 +7645,15 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' @@ -7602,6 +7665,33 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] @@ -7622,36 +7712,19 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7676,8 +7749,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -7685,7 +7756,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7698,12 +7768,25 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -7723,6 +7806,60 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, + from /usr/include/c++/13/bits/allocator.h:46, + from /usr/include/c++/13/string:43, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, + from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, + from /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 577 | *mutable_child(i) = c; + | ~~~~~~~~~~~~~~~~~~^~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] + 578 | c->fields_.parent = this; + | ~~~~~~~~~~~~~~~~~~^~~~~~ +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', + inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, + inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: +/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -7761,66 +7898,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, - from /usr/include/c++/13/bits/allocator.h:46, - from /usr/include/c++/13/string:43, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, - from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, - from /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -7840,29 +7917,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 577 | *mutable_child(i) = c; - | ~~~~~~~~~~~~~~~~~~^~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] - 578 | c->fields_.parent = this; - | ~~~~~~~~~~~~~~~~~~^~~~~~ -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', - inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, - inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: -/usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7881,6 +7935,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7899,7 +7954,7 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7937,7 +7992,6 @@ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -7957,6 +8011,15 @@ 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] + 565 | ++vptr; + | ^~ +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] @@ -8063,33 +8126,6 @@ /usr/include/c++/13/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-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] - 565 | ++vptr; - | ^~ -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] @@ -8279,156 +8315,156 @@ make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make 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"--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd 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ext/bamtools/api/CMakeFiles/BamTools.dir/build -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Built target mimalloc-obj +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make 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]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Built target coverage_model -[ 4%] Built target gqf -[ 24%] Built target BamTools -[ 26%] Built target format -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend -[ 48%] Built target llvm-support -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend -[ 51%] Built target edlib -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" -[ 51%] Built target gtest -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.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-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.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-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 51%] Built target binary_io -[ 58%] Built target samtools +[ 9%] Built target format +[ 9%] Built target mimalloc-obj +[ 9%] Built target version +[ 9%] Built target gqf +[ 12%] Built target gtest +[ 12%] Built target edlib +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -[ 60%] Built target version -[ 60%] Built target paired_info -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -[ 63%] Built target sequence make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +[ 12%] Built target binary_io +[ 12%] Built target coverage_model +[ 12%] Built target paired_info make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 31%] Built target BamTools +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 53%] Built target llvm-support make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 63%] Built target teamcity_gtest make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target input -[ 70%] Built target utils +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +[ 53%] Built target teamcity_gtest +[ 56%] Built target sequence +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 58%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +[ 65%] Built target samtools +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 70%] Built target input [ 75%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend @@ -8437,9 +8473,9 @@ make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -8481,22 +8517,22 @@ make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 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/binary_test.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/quality_test.cpp -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/nucl_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o -cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp +cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp In file included from /build/reproducible-path/spades-3.15.5+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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, @@ -8705,10 +8741,10 @@ make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_test -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j20 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu @@ -8737,7 +8773,7 @@ 1: [ RUN ] Seq.Selector 1: [ OK ] Seq.Selector (0 ms) 1: [ RUN ] Seq.ShiftLeft -1: [ OK ] Seq.ShiftLeft (0 ms) +1: [ OK ] Seq.ShiftLeft (1 ms) 1: [ RUN ] Seq.ShiftRight 1: [ OK ] Seq.ShiftRight (0 ms) 1: [ RUN ] Seq.Str @@ -8873,7 +8909,7 @@ 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 0.01 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. @@ -8884,23 +8920,23 @@ 2: [ OK ] GraphCore.Empty (1 ms) 2: [ RUN ] GraphCore.OneVertex 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) 2: [----------] 6 tests from GraphCore (1 ms total) 2: @@ -8935,10 +8971,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.001 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (71 ms) -2: [----------] 13 tests from PairedInfo (71 ms total) +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] PairedInfo.RandomSymmetry (37 ms) +2: [----------] 13 tests from PairedInfo (37 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial @@ -8981,854 +9017,854 @@ 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest -2: 0:00:00.072 1M / 9M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.077 1M / 9M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.079 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: 0:00:00.079 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.082 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (12 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: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (4 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.083 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.084 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.084 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: 0:00:00.084 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.084 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.084 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: 0:00:00.042 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.042 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.042 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: 0:00:00.042 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.042 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.042 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.085 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.085 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.085 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.085 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.085 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.086 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance +2: 0:00:00.042 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.043 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.043 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.043 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.043 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.043 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (1 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.086 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.086 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.086 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: 0:00:00.086 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: 0:00:00.132 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (76 ms) +2: 0:00:00.043 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.043 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.043 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: 0:00:00.043 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: 0:00:00.066 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (38 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:00.161 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.162 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.162 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: 0:00:00.162 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: 0:00:00.202 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (69 ms) +2: 0:00:00.082 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.082 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.082 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: 0:00:00.082 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: 0:00:00.101 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (35 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:00.231 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.231 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.231 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: 0:00:00.231 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: 0:00:00.266 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (64 ms) +2: 0:00:00.117 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.117 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.117 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: 0:00:00.117 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: 0:00:00.135 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (34 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:00.295 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.295 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.296 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: 0:00:00.296 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: 0:00:00.336 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:00.336 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: 0:00:00.349 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (83 ms) +2: 0:00:00.151 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.151 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.151 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: 0:00:00.151 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: 0:00:00.166 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.166 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: 0:00:00.174 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (40 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:00.378 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.378 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.378 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: 0:00:00.378 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:00.406 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:00.406 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (80 ms) +2: 0:00:00.190 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.190 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.190 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: 0:00:00.190 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:00.203 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:00.203 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (44 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:00.458 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.458 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.458 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: 0:00:00.458 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.459 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.459 1M / 61M INFO General (simplification_test.cpp : 276) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (2 ms) +2: 0:00:00.234 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.234 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.234 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: 0:00:00.234 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.235 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.235 1M / 61M INFO General (simplification_test.cpp : 276) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:00.459 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.459 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.459 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.460 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: 0:00:00.460 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.492 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:00.492 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:00.535 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:00.639 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: 0:00:00.639 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:00.693 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:00.693 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (286 ms) +2: 0:00:00.235 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.235 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.235 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.235 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: 0:00:00.235 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.251 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.251 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.280 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.339 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: 0:00:00.339 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.369 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.369 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (162 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:00.746 1M / 63M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.746 1M / 63M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.746 1M / 63M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.746 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: 0:00:00.746 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: 0:00:00.923 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:00.924 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) -2: 0:00:00.957 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.002 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: 0:00:01.002 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.050 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:01.050 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 (351 ms) +2: 0:00:00.397 1M / 64M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.397 1M / 64M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.397 1M / 64M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.397 1M / 64M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp +2: 0:00:00.397 1M / 64M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.492 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:00.493 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) +2: 0:00:00.517 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.562 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). +2: 0:00:00.562 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.591 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.591 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 (222 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:01.097 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.097 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.097 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.097 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: 0:00:01.097 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: 0:00:01.099 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:01.099 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) -2: 0:00:01.105 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.157 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: 0:00:01.161 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.185 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:01.186 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:01.186 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (155 ms) +2: 0:00:00.620 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.620 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.620 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.620 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp +2: 0:00:00.620 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.622 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.622 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) +2: 0:00:00.627 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.661 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:00.661 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.672 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.672 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.672 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (94 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:01.252 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.252 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.252 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.252 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: 0:00:01.252 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.293 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:01.294 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:01.342 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.437 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:01.438 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.494 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.494 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:01.494 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (294 ms) +2: 0:00:00.714 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.714 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.714 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.714 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.714 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.731 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.731 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:00.758 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.817 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: 0:00:00.817 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.845 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.845 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.846 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (159 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:01.545 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.545 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.545 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.546 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: 0:00:01.546 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:01.546 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:01.546 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) -2: 0:00:01.546 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.549 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: 0:00:01.549 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.550 3M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:01.550 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:01.550 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (17 ms) +2: 0:00:00.872 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.872 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.872 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.872 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:00.872 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:00.873 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:00.873 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) +2: 0:00:00.873 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.875 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:00.875 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.875 3M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.875 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:00.876 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (12 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:01.563 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.563 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.563 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.563 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:01.563 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:01.563 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:01.564 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) -2: 0:00:01.564 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.565 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: 0:00:01.565 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.565 1M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:01.565 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:01.565 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (4 ms) +2: 0:00:00.884 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.884 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.884 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.884 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.884 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.884 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.884 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) +2: 0:00:00.884 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.885 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:00.885 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.885 1M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.885 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.885 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (2 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:01.567 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.567 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.567 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.567 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: 0:00:01.567 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:01.568 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:01.568 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) -2: 0:00:01.569 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.577 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: 0:00:01.577 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.580 4M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:01.581 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:01.581 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (34 ms) +2: 0:00:00.886 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.886 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.886 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.886 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:00.886 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:00.887 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:00.887 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) +2: 0:00:00.887 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.892 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:00.892 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.894 4M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.894 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:00.894 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (21 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:01.602 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.602 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.602 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.602 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:01.602 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:01.602 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:01.603 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) -2: 0:00:01.603 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.603 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: 0:00:01.603 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.604 2M / 154M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:01.604 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (3 ms) -2: [----------] 17 tests from Simplification (1533 ms total) +2: 0:00:00.907 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.907 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.907 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.907 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:00.907 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:00.907 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:00.907 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) +2: 0:00:00.907 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.908 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:00.908 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:00.908 2M / 154M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:00.908 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (1 ms) +2: [----------] 17 tests from Simplification (871 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:01.604 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.604 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.605 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.605 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.605 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.605 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.605 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.622 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads -2: 0:00:01.622 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.624 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:01.624 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.624 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.625 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.625 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.625 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.638 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. -2: 0:00:01.638 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.641 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. -2: 0:00:01.641 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.642 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: 0:00:01.642 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.643 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.643 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.643 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.643 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.643 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:01.643 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.643 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:01.643 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (40 ms) +2: 0:00:00.908 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.908 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.908 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.908 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.908 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.908 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.908 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.914 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads +2: 0:00:00.914 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.915 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:00.916 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.916 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.916 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.916 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.916 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.918 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. +2: 0:00:00.918 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.919 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. +2: 0:00:00.919 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.920 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:00.920 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.920 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.920 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.920 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:00.921 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.921 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.921 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (13 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:01.645 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.645 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.645 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.645 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.645 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.646 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.646 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.656 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:01.656 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.659 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. -2: 0:00:01.659 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.659 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.660 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.660 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.660 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.671 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. -2: 0:00:01.671 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.674 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. -2: 0:00:01.674 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.675 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: 0:00:01.675 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.676 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.676 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.676 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.677 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.677 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:01.677 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.677 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:01.677 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (32 ms) +2: 0:00:00.921 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.921 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.921 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.921 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.921 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.921 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.921 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.925 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.925 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.926 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. +2: 0:00:00.926 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.926 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.926 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.926 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.926 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.929 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. +2: 0:00:00.929 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.930 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. +2: 0:00:00.930 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.931 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:00.931 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.931 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.931 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.931 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.931 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.931 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:00.931 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.931 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.931 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:00.931 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.931 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.931 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.932 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.932 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (11 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:01.678 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.678 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.678 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.678 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.678 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.678 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.678 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.691 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:01.692 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.695 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:01.696 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.696 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.696 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.696 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.696 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.707 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:01.707 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.711 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:01.711 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.712 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: 0:00:01.712 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.712 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.713 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.713 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.714 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.714 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:01.714 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.714 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:01.714 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (37 ms) +2: 0:00:00.932 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.932 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.932 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.932 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.932 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.932 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.932 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.934 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.934 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.936 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.936 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.936 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.936 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.936 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.936 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.938 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:00.938 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.939 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.939 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.940 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:00.940 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.940 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.941 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.941 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.941 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.941 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.941 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.941 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:00.941 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (9 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:01.715 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.715 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.715 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.715 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.715 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.715 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.715 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.727 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:01.727 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.729 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:01.730 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.730 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.730 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.730 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.730 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.741 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:01.741 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.743 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:01.743 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.744 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: 0:00:01.745 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.745 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.746 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.746 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.746 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.746 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:01.746 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.746 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.746 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create -2: 0:00:01.746 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.746 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.747 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.747 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:01.747 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (33 ms) +2: 0:00:00.941 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.941 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.941 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.941 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.941 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.941 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.941 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.944 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.944 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.945 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.945 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.945 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.945 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.945 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.945 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.948 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:00.948 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.949 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:00.949 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.950 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:00.950 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.950 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.951 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.951 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.951 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.951 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:00.951 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.951 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:00.951 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (10 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:01.747 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.747 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.747 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.747 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.748 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.748 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.748 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.761 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:01.761 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.764 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:01.764 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.764 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.764 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.764 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.764 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.778 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. -2: 0:00:01.778 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.780 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:01.780 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.783 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: 0:00:01.783 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.784 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.784 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.784 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.784 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.784 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:01.785 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.785 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:01.785 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (38 ms) +2: 0:00:00.951 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.951 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.951 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.951 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.951 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.951 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.951 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.955 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:00.955 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.956 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.957 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.957 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.957 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.957 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.957 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.960 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. +2: 0:00:00.960 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.962 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:00.962 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.963 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:00.963 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.963 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.963 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.963 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.963 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.963 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:00.963 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.963 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:00.963 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (13 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:01.786 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.786 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.786 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.786 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.786 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.786 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.786 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.802 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:01.803 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.808 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.808 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.808 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.808 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.808 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.808 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.820 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:01.821 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.824 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.824 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.825 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: 0:00:01.825 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.825 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.826 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.826 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.826 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.826 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:01.826 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.826 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:01.826 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (42 ms) +2: 0:00:00.964 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.964 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.964 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.964 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.964 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.964 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.964 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.968 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.968 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.969 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.969 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.969 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.969 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.970 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.970 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.973 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.973 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.974 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.974 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.974 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.974 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.975 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.975 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.975 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.975 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.975 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.975 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.975 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.975 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (11 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:01.828 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.828 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.828 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.828 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.828 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.829 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.829 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.829 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.842 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:01.843 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.846 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.846 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.846 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.846 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.846 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.846 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.859 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:01.859 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.862 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.862 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.863 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: 0:00:01.863 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.865 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.865 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.865 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.865 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.865 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:01.865 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.865 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.865 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:01.865 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.865 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.865 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.865 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:01.866 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:01.866 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:01.866 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:01.866 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.866 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: 0:00:01.866 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (38 ms) +2: 0:00:00.976 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.976 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.976 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.976 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.976 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.976 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.976 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.976 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.980 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.980 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.982 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.982 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.982 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.982 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.982 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.982 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.985 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.985 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.986 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.987 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.987 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.987 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.988 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.988 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.988 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.988 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.988 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.988 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.988 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.988 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:00.988 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:00.988 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:00.988 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.988 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:00.988 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (13 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:01.866 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.866 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.866 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.866 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:01.867 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.867 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.867 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.867 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.882 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:01.882 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.886 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.886 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.886 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.886 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.886 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.886 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.901 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:01.901 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.904 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:01.904 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.905 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: 0:00:01.905 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.906 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.907 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.907 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.907 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.907 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:01.907 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.907 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:01.907 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:01.915 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:01.915 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:01.915 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.915 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: 0:00:01.915 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (49 ms) +2: 0:00:00.988 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.989 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.989 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:00.989 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:00.989 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.989 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.989 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.989 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.992 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:00.992 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.993 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.994 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:00.994 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:00.994 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:00.994 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:00.994 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:00.997 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:00.997 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:00.998 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:00.998 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:00.998 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:00.998 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:00.999 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:00.999 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:00.999 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:00.999 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:00.999 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:00.999 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:00.999 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:00.999 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:01.000 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:01.000 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:01.000 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.000 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: 0:00:01.000 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (12 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:01.916 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.916 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.916 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.916 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 -2: 0:00:01.916 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.916 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.916 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.916 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.928 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:01.929 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.931 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. -2: 0:00:01.931 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:01.931 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:01.931 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:01.931 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:01.931 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:01.943 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. -2: 0:00:01.943 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:01.946 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:01.946 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.947 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: 0:00:01.947 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:01.948 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:01.949 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:01.949 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:01.949 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:01.950 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:01.950 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:01.950 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create -2: 0:00:01.950 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:01.950 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:01.950 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) -2: 0:00:01.950 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.950 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: 0:00:01.950 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.950 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index -2: 0:00:01.950 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.951 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: 0:00:01.951 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:01.951 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM -2: 0:00:01.951 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:01.951 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done -2: 0:00:01.977 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (79 ms) -2: [----------] 9 tests from GraphConstruction (390 ms total) +2: 0:00:01.000 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.000 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.000 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.000 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 +2: 0:00:01.000 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.000 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:01.000 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.000 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:01.003 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:01.003 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:01.004 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. +2: 0:00:01.004 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:01.004 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.005 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:01.005 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.005 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:01.008 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. +2: 0:00:01.008 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:01.009 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:01.009 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.009 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: 0:00:01.009 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:01.010 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:01.010 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.010 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:01.010 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:01.010 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:01.010 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:01.010 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create +2: 0:00:01.010 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:01.010 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:01.010 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) +2: 0:00:01.010 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.010 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: 0:00:01.010 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.010 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index +2: 0:00:01.010 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.011 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: 0:00:01.011 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:01.011 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM +2: 0:00:01.011 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:01.011 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done +2: 0:00:01.015 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (17 ms) +2: [----------] 9 tests from GraphConstruction (109 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order -2: 0:00:01.994 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.994 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.057 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.057 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (62 ms) +2: 0:00:01.018 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.018 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.054 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.055 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (37 ms) 2: [ RUN ] Io.PairedInfo -2: [ OK ] Io.PairedInfo (9 ms) +2: [ OK ] Io.PairedInfo (4 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) -2: [----------] 3 tests from Io (71 ms total) +2: [----------] 3 tests from Io (41 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:02.066 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.066 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.066 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: 0:00:02.066 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.066 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.058 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.058 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.067 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: 0:00:02.067 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.067 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.067 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: 0:00:02.067 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.067 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (1 ms) +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.067 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.067 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: 0:00:02.067 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.068 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.059 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.059 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:02.068 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.068 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.068 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: 0:00:02.068 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.068 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSubpaths (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate -2: 0:00:02.068 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.068 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.068 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: 0:00:02.068 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.068 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (1 ms) +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.069 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: 0:00:02.069 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.069 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.069 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: 0:00:02.069 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.069 1M / 154M 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 (4 ms total) +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) +2: [----------] 8 tests from PathExtend (2 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.069 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.069 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: 0:00:02.070 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.070 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicNoDiff (1 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:02.070 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.070 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.070 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: 0:00:02.070 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.070 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicDiff (1 ms) +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:02.070 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.070 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.070 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: 0:00:02.070 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:02.071 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:02.071 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.061 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.061 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.061 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:02.071 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.071 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.071 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: 0:00:02.071 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.078 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.078 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (8 ms) +2: 0:00:01.062 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.062 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.062 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.062 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.066 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.067 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:02.078 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.078 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.078 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:02.078 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.085 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.085 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (7 ms) +2: 0:00:01.067 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.067 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.067 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.067 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.071 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.071 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:02.086 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.086 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.086 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: 0:00:02.086 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.092 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.092 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.093 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (7 ms) +2: 0:00:01.071 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.071 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.071 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: 0:00:01.071 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.076 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.076 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.076 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:02.093 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.093 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.093 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: 0:00:02.093 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.100 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.100 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (7 ms) +2: 0:00:01.076 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.076 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.076 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.076 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.081 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.081 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:02.100 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.100 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.100 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: 0:00:02.100 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.107 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.107 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.107 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (7 ms) +2: 0:00:01.081 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.081 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.081 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.081 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.085 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.085 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.085 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:02.107 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.107 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.107 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: 0:00:02.107 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.114 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.114 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.114 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (8 ms) +2: 0:00:01.085 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.085 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.085 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.085 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.090 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.090 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.090 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:02.114 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.114 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.114 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: 0:00:02.114 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.121 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.121 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.121 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (7 ms) +2: 0:00:01.090 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.090 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.090 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.090 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.094 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.095 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.095 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:02.122 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.122 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.122 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: 0:00:02.122 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.129 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.129 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.129 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (7 ms) +2: 0:00:01.095 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.095 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.095 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.095 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.099 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.099 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.099 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (5 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:02.129 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.129 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.129 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:02.129 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.136 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (7 ms) +2: 0:00:01.099 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.099 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.099 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.099 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.104 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (5 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:02.136 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.136 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.136 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: 0:00:02.136 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.143 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (8 ms) +2: 0:00:01.104 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.104 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.104 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.104 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.108 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:02.144 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.144 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.144 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: 0:00:02.144 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.151 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (8 ms) +2: 0:00:01.109 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.109 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.109 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.109 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.113 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:02.152 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.152 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.152 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: 0:00:02.152 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.159 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (7 ms) +2: 0:00:01.113 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.113 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.113 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.113 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.118 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:02.159 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.159 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.159 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: 0:00:02.159 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.166 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (8 ms) +2: 0:00:01.118 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.118 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.118 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.118 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.122 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:02.167 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.167 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.167 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: 0:00:02.167 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.174 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (8 ms) +2: 0:00:01.122 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.122 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.122 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.122 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.127 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (5 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:02.175 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.175 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.175 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: 0:00:02.175 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.182 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.182 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.182 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (8 ms) +2: 0:00:01.127 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.127 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.127 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.127 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.132 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.132 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.132 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:02.182 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.182 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.182 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: 0:00:02.182 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.189 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.189 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.189 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (6 ms) +2: 0:00:01.132 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.132 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.132 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.132 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.136 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.136 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.136 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (5 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:02.189 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.189 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.189 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: 0:00:02.189 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.195 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.195 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.195 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (7 ms) +2: 0:00:01.136 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.136 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.136 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.136 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.141 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.141 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.141 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (5 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:02.195 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.195 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.196 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: 0:00:02.196 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.202 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.202 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.202 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (7 ms) +2: 0:00:01.141 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.141 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.141 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.141 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.145 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.146 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.146 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (4 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:02.203 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.203 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.203 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: 0:00:02.203 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.209 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.209 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.209 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (7 ms) +2: 0:00:01.146 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.146 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.146 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.146 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.150 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.150 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.150 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (5 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:02.210 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.210 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.210 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: 0:00:02.210 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.217 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.217 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:02.217 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (7 ms) -2: [----------] 23 tests from OverlapRemoval (147 ms total) +2: 0:00:01.150 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.150 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.150 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.150 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.155 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.155 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:01.155 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (5 ms) +2: [----------] 23 tests from OverlapRemoval (95 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:02.217 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 +2: 0:00:01.155 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:02.217 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 -2: 0:00:02.217 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 +2: 0:00:01.155 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 +2: 0:00:01.155 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:02.217 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.217 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.217 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: 0:00:02.217 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.225 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:02.238 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (720 ms) +2: 0:00:01.155 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.155 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.155 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.155 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.159 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.167 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (426 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:02.938 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.938 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.938 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: 0:00:02.938 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.945 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (8 ms) +2: 0:00:01.581 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.581 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.581 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.581 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.586 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraOneEdgeTest (5 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest -2: 0:00:02.945 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.945 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.945 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: 0:00:02.946 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:02.952 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraGrowEndsTest (7 ms) -2: [----------] 5 tests from GraphAligner (736 ms total) +2: 0:00:01.586 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.586 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.586 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.586 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.590 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraGrowEndsTest (5 ms) +2: [----------] 5 tests from GraphAligner (436 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 98 tests from 10 test suites ran. (2953 ms total) +2: [==========] 98 tests from 10 test suites ran. (1592 ms total) 2: [ PASSED ] 98 tests. -2/2 Test #2: debruijn_test .................... Passed 2.96 sec +2/2 Test #2: debruijn_test .................... Passed 1.60 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 2.98 sec +Total Test time (real) = 1.60 sec make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -9851,30 +9887,30 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/manual.html -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/truspades_manual.html @@ -9883,27 +9919,27 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/GPLv2.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/hammer/config.info @@ -9933,49 +9969,49 @@ -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/correction_iteration_script.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors --- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py +-- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install @@ -10032,12 +10068,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/310429/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/310429/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/3053116 and its subdirectories -I: Current time: Fri May 10 06:49:25 -12 2024 -I: pbuilder-time-stamp: 1715366965 +I: removing directory /srv/workspace/pbuilder/310429 and its subdirectories +I: Current time: Fri Jun 13 15:21:14 +14 2025 +I: pbuilder-time-stamp: 1749777674