Diff of the two buildlogs: -- --- b1/build.log 2024-11-15 23:18:46.363987342 +0000 +++ b2/build.log 2024-11-15 23:29:04.047904795 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 15 10:56:27 -12 2024 -I: pbuilder-time-stamp: 1731711387 +I: Current time: Fri Dec 19 19:41:50 +14 2025 +I: pbuilder-time-stamp: 1766122910 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -44,52 +44,84 @@ dpkg-source: info: applying deactivate_tests_with_no_data.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2534532/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3857398/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 Dec 19 05:42 /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/3857398/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3857398/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='experimental' - 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='eee0c785d7f24c90b9ffd8129d547911' - 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='2534532' - PS1='# ' - PS2='> ' + INVOCATION_ID=c74110d0c1454757968e361c979fa617 + 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=3857398 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.CN7MoEam/pbuilderrc_H7by --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CN7MoEam/b1 --logfile b1/build.log spades_4.0.0+dfsg1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://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.CN7MoEam/pbuilderrc_oRH9 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CN7MoEam/b2 --logfile b2/build.log spades_4.0.0+dfsg1-1.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 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2534532/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3857398/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -401,7 +433,7 @@ Get: 220 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.0-2 [730 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-5 [216 kB] -Fetched 238 MB in 13s (18.9 MB/s) +Fetched 238 MB in 3s (79.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) @@ -1125,8 +1157,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Nov 15 22:58:42 UTC 2024. -Universal Time is now: Fri Nov 15 22:58:42 UTC 2024. +Local time is now: Fri Dec 19 05:43:29 UTC 2025. +Universal Time is now: Fri Dec 19 05:43:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2+b1) ... @@ -1326,7 +1358,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/spades-4.0.0+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_4.0.0+dfsg1-1_source.changes +I: user script /srv/workspace/pbuilder/3857398/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/3857398/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/spades-4.0.0+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_4.0.0+dfsg1-1_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+dfsg1-1 dpkg-buildpackage: info: source distribution experimental @@ -1731,7 +1767,7 @@ -- Configured C++11 for multithreading. -- Configuring Vectorization : ON -- Automatic Cache Size Configuration --- Configuring Cache Size : 524288UL +-- Configuring Cache Size : 4194304UL -- Blaze has been configured successfully -- Enabling BayesHammer as a dependency to SPAdes -- Enabling IonHammer as a dependency to SPAdes @@ -1747,8 +1783,8 @@ -- mts project is disabled -- online_vis project is disabled -- cds_subgraphs project is disabled --- Configuring done (96.8s) --- Generating done (0.7s) +-- Configuring done (20.6s) +-- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: @@ -1761,7 +1797,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' 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-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1772,113 +1808,165 @@ make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend -make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/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 -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-4.0.0+dfsg1/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 cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" +make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 0%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o -[ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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-cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/format.cc make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APInt.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Atomic.cpp +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o -[ 3%] Building CXX object 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ext/cppformat/CMakeFiles/format.dir/format.cc.o +[ 1%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o +[ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o +[ 1%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o +[ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o +[ 1%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +[ 1%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o +[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o [ 2%] Building CXX object ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o -[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -[ 2%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o -[ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -cd 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o -MF CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/adler32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32_fold.c -[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -[ 2%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o -[ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o -cd 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/format.cc +[ 4%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ 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common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o +[ 4%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o -MF CMakeFiles/zlibstatic.dir/compare256.c.o.d -o CMakeFiles/zlibstatic.dir/compare256.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compare256.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/version.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o -MF CMakeFiles/zlibstatic.dir/chunkset.c.o.d -o CMakeFiles/zlibstatic.dir/chunkset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/chunkset.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp +[ 7%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/APFloat.cpp +[ 7%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o +[ 7%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o -MF CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/adler32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32_fold.c +[ 8%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -ftls-model=initial-exec 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CMakeFiles/zlibstatic.dir/compress.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compress.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Atomic.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o -MF CMakeFiles/zlibstatic.dir/cpu_features.c.o.d -o CMakeFiles/zlibstatic.dir/cpu_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/cpu_features.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Debug.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o -MF CMakeFiles/easel.dir/esl_bitfield.c.o.d -o CMakeFiles/easel.dir/esl_bitfield.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_bitfield.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Errno.cpp +[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o -MF CMakeFiles/zlibstatic.dir/deflate.c.o.d -o CMakeFiles/zlibstatic.dir/deflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate.c +[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o -MF CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_fast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_fast.c +[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cluster.c +[ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o -MF CMakeFiles/easel.dir/esl_arr3.c.o.d -o CMakeFiles/easel.dir/esl_arr3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr3.c +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o -MF CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_huff.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_huff.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:612:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 612 | printf("%02llx ", j); @@ -1920,177 +2008,338 @@ | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o -MF CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_medium.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_medium.c +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_composition.c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_deserialize': +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1609:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1609 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:1618:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1618 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX static library liblexy_file.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -P CMakeFiles/lexy_file.dir/cmake_clean_target.cmake -[ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o -[ 6%] Linking CXX static library libversion.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o -MF CMakeFiles/zlibstatic.dir/compare256.c.o.d -o CMakeFiles/zlibstatic.dir/compare256.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compare256.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lexy_file.dir/link.txt --verbose=1 -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 -[ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o -MF CMakeFiles/zlibstatic.dir/compress.c.o.d -o CMakeFiles/zlibstatic.dir/compress.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/compress.c -[ 7%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o -MF CMakeFiles/zlibstatic.dir/cpu_features.c.o.d -o CMakeFiles/zlibstatic.dir/cpu_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/cpu_features.c -[ 8%] Built target lexy_file -make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend -/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o -/usr/bin/ranlib libversion.a -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu 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_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid.c -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 8%] Built target version -[ 8%] Building CXX object common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -MF CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d -o CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.cpp -[ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 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_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -MF CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_braid_comb.c -[ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o -MF CMakeFiles/zlibstatic.dir/crc32_fold.c.o.d -o CMakeFiles/zlibstatic.dir/crc32_fold.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/crc32_fold.c -[ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o -MF CMakeFiles/zlibstatic.dir/deflate.c.o.d -o CMakeFiles/zlibstatic.dir/deflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate.c -[ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o -MF CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_fast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_fast.c -[ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alloc.c.o -MF CMakeFiles/easel.dir/esl_alloc.c.o.d -o CMakeFiles/easel.dir/esl_alloc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_alloc.c -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o -MF CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_huff.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_huff.c -[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ErrorHandling.cpp -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o -MF CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_medium.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_medium.c -[ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_alphabet.c -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o -MF CMakeFiles/zlibstatic.dir/deflate_quick.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_quick.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_quick.c -[ 9%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/genomic_info.cpp -[ 9%] Linking C static library libgqf.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 -[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FoldingSet.cpp -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o +[ 10%] Linking CXX static library libversion.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o -MF CMakeFiles/zlibstatic.dir/deflate_rle.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_rle.c -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o -MF CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_slow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_slow.c -[ 9%] Linking CXX static library libmph_index.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake -/usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o -/usr/bin/ranlib libgqf.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 -[ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/FormatVariadic.cpp -[ 9%] Built target gqf -[ 9%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o -MF CMakeFiles/zlibstatic.dir/deflate_stored.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_stored.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_stored.c -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o +[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o -MF CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d -o CMakeFiles/zlibstatic.dir/deflate_slow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/deflate_slow.c +[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o -MF CMakeFiles/zlibstatic.dir/functable.c.o.d -o CMakeFiles/zlibstatic.dir/functable.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/functable.c +[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/infback.c.o -MF CMakeFiles/zlibstatic.dir/infback.c.o.d -o CMakeFiles/zlibstatic.dir/infback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/infback.c -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o +[ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Hashing.cpp +[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inflate.c.o -MF CMakeFiles/zlibstatic.dir/inflate.c.o.d -o CMakeFiles/zlibstatic.dir/inflate.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inflate.c -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o +[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o +[ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o -MF CMakeFiles/zlibstatic.dir/insert_string.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string.c +[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Host.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o -MF CMakeFiles/zlibstatic.dir/inftrees.c.o.d -o CMakeFiles/zlibstatic.dir/inftrees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/inftrees.c -/usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o -/usr/bin/ranlib libmph_index.a +[ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o -MF CMakeFiles/easel.dir/esl_cpu.c.o.d -o CMakeFiles/easel.dir/esl_cpu.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cpu.c +/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o +/usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 10%] Built target mph_index -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o -MF CMakeFiles/zlibstatic.dir/insert_string.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string.c -[ 10%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o +[ 12%] Built target version +[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dirichlet.c +[ 13%] Linking CXX static library liblexy_file.a +[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LineIterator.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -P CMakeFiles/lexy_file.dir/cmake_clean_target.cmake +[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MD5.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lexy_file.dir/link.txt --verbose=1 +[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ManagedStatic.cpp +[ 14%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o -MF CMakeFiles/zlibstatic.dir/slide_hash.c.o.d -o CMakeFiles/zlibstatic.dir/slide_hash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/slide_hash.c -[ 12%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem 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+make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 15%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Path.cpp +[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_exponential.c +[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Program.cpp +[ 17%] Linking CXX static library libmph_index.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake +[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Regex.cpp +[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Signals.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 +[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SmallVector.cpp +[ 18%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mxsave -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/x86_features.c -[ 12%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gencode.c +/usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o +/usr/bin/ranlib libmph_index.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SourceMgr.cpp +[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o +[ 19%] Built target mph_index cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o -c 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-DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_avx2.c -[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr2.c.o -MF CMakeFiles/easel.dir/esl_arr2.c.o.d -o CMakeFiles/easel.dir/esl_arr2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr2.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 -[ 13%] Building C object ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_arr3.c.o -MF CMakeFiles/easel.dir/esl_arr3.c.o.d -o CMakeFiles/easel.dir/esl_arr3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_arr3.c -[ 13%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringExtras.cpp +[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx2.c +[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_avx2.c -[ 14%] Building C object ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_bitfield.c.o -MF CMakeFiles/easel.dir/esl_bitfield.c.o.d -o CMakeFiles/easel.dir/esl_bitfield.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_bitfield.c -[ 14%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gev.c +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_graph.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_graph.c.o -MF CMakeFiles/easel.dir/esl_graph.c.o.d -o CMakeFiles/easel.dir/esl_graph.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_graph.c +[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512.c +[ 20%] Linking C static library libgqf.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake +[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512_vnni.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gumbel.c +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG 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+/usr/bin/ranlib libgqf.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_heap.c +[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o +[ 20%] Built target gqf +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -c 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ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringRef.cpp +[ 23%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -c 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ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringSaver.cpp +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_histogram.c +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hmm.c +[ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_sse2.c +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ThreadLocal.cpp +[ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_sse2.c +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o -MF CMakeFiles/easel.dir/esl_huffman.c.o.d -o CMakeFiles/easel.dir/esl_huffman.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_huffman.c +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Threading.cpp +[ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_sse2.c +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hyperexp.c +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/TimeProfiler.cpp +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Twine.cpp +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Unicode.cpp +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp:100: +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] + 94 | mi = ::mallinfo(); + | ~~~~~~~~~~^~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:35: +/usr/include/malloc.h:114:24: note: declared here + 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; + | ^~~~~~~~ +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_iset.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_iset.c.o -MF CMakeFiles/easel.dir/esl_iset.c.o.d -o CMakeFiles/easel.dir/esl_iset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_iset.c +[ 25%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_ssse3.c +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_json.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/WithColor.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_json.c.o -MF CMakeFiles/easel.dir/esl_json.c.o.d -o CMakeFiles/easel.dir/esl_json.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_json.c +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLParser.cpp +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLTraits.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_keyhash.c +[ 28%] Linking CXX static library libteamcity_gtest.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 +[ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o -MF CMakeFiles/easel.dir/esl_lognormal.c.o.d -o CMakeFiles/easel.dir/esl_lognormal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_lognormal.c +[ 28%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_os_ostream.cpp +[ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o -MF CMakeFiles/easel.dir/esl_matrixops.c.o.d -o CMakeFiles/easel.dir/esl_matrixops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_matrixops.c +[ 28%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_ssse3.c +/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +/usr/bin/ranlib libteamcity_gtest.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 28%] Built target teamcity_gtest +[ 29%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_pclmulqdq.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mem.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_minimizer.c +[ 29%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_vpclmulqdq.c +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_ostream.cpp +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o -MF CMakeFiles/easel.dir/esl_mixdchlet.c.o.d -o CMakeFiles/easel.dir/esl_mixdchlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixdchlet.c +[ 30%] Linking CXX static library libedlib.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 +[ 30%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regcomp.c +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixgev.c +[ 31%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regerror.c +[ 31%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o -MF CMakeFiles/zlibstatic.dir/gzlib.c.o.d -o CMakeFiles/zlibstatic.dir/gzlib.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzlib.c /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 14%] Built target edlib +[ 31%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o -MF CMakeFiles/zlibstatic.dir/gzread.c.o.d -o CMakeFiles/zlibstatic.dir/gzread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/gzread.c +[ 31%] Built target edlib +[ 31%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -MF CMakeFiles/zlibstatic.dir/gzwrite.c.o.d -o CMakeFiles/zlibstatic.dir/gzwrite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzwrite.c +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mpi.c +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msa.c +[ 31%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Host.cpp +[ 31%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regfree.c +[ 31%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regstrlcpy.c +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/sequence_tools.cpp -[ 14%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc 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ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/JSON.cpp -[ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx2.c -[ 15%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LEB128.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_avx512_vnni.c -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_composition.c -[ 15%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LineIterator.cpp -[ 17%] Linking CXX static library libteamcity_gtest.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cpu.c.o -MF CMakeFiles/easel.dir/esl_cpu.c.o.d -o CMakeFiles/easel.dir/esl_cpu.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_cpu.c -/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 +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -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 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ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_phylip.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_selex.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_stockholm.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msaweight.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_normal.c +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_paml.c +[ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o +[ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_quicksort.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_random.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o -MF CMakeFiles/easel.dir/esl_rand64.c.o.d -o CMakeFiles/easel.dir/esl_rand64.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rand64.c +[ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_randomseq.c +[ 36%] Linking C static library libz.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -P CMakeFiles/zlibstatic.dir/cmake_clean_target.cmake +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ratematrix.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o -MF CMakeFiles/easel.dir/esl_red_black.c.o.d -o CMakeFiles/easel.dir/esl_red_black.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_red_black.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cmake -E cmake_link_script CMakeFiles/zlibstatic.dir/link.txt --verbose=1 +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_regexp.c +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rootfinder.c +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sq.c +[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ascii.c +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:364:10: warning: unused variable 'loaded' [-Wunused-variable] + 364 | bool loaded = base::BinRead(is, gp); + | ^~~~~~ +/usr/bin/ar qc libz.a CMakeFiles/zlibstatic.dir/adler32.c.o CMakeFiles/zlibstatic.dir/adler32_fold.c.o CMakeFiles/zlibstatic.dir/chunkset.c.o CMakeFiles/zlibstatic.dir/compare256.c.o CMakeFiles/zlibstatic.dir/compress.c.o CMakeFiles/zlibstatic.dir/cpu_features.c.o CMakeFiles/zlibstatic.dir/crc32_braid.c.o CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o CMakeFiles/zlibstatic.dir/crc32_fold.c.o CMakeFiles/zlibstatic.dir/deflate.c.o CMakeFiles/zlibstatic.dir/deflate_fast.c.o CMakeFiles/zlibstatic.dir/deflate_huff.c.o CMakeFiles/zlibstatic.dir/deflate_medium.c.o CMakeFiles/zlibstatic.dir/deflate_quick.c.o CMakeFiles/zlibstatic.dir/deflate_rle.c.o CMakeFiles/zlibstatic.dir/deflate_slow.c.o CMakeFiles/zlibstatic.dir/deflate_stored.c.o CMakeFiles/zlibstatic.dir/functable.c.o CMakeFiles/zlibstatic.dir/infback.c.o CMakeFiles/zlibstatic.dir/inflate.c.o CMakeFiles/zlibstatic.dir/inftrees.c.o CMakeFiles/zlibstatic.dir/insert_string.c.o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o CMakeFiles/zlibstatic.dir/slide_hash.c.o CMakeFiles/zlibstatic.dir/trees.c.o CMakeFiles/zlibstatic.dir/uncompr.c.o CMakeFiles/zlibstatic.dir/zutil.c.o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o CMakeFiles/zlibstatic.dir/gzlib.c.o CMakeFiles/zlibstatic.dir/gzread.c.o CMakeFiles/zlibstatic.dir/gzwrite.c.o +/usr/bin/ranlib libz.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 17%] Built target teamcity_gtest -[ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_sse42.c -[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dirichlet.c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:326:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] 326 | if (converged_ && Valley_ > x[2] && x[2] > 2) { @@ -2098,22 +2347,35 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.cpp:360:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 360 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? | ^~~~~~~ -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_distance.c -[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/insert_string_sse42.c -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:364:10: warning: unused variable 'loaded' [-Wunused-variable] - 364 | bool loaded = base::BinRead(is, gp); - | ^~~~~~ -[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dmatrix.c -[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_sse2.c -[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/compare256_sse2.c +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o +[ 39%] Built target zlibstatic +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kstring.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stopwatch.c +[ 40%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_aux.c +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o +[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stretchexp.c +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o -MF CMakeFiles/easel.dir/esl_subcmd.c.o.d -o CMakeFiles/easel.dir/esl_subcmd.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_subcmd.c +[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_import.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/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]': @@ -2186,189 +2448,253 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:131:14: warning: unused variable 'loaded' [-Wunused-variable] 131 | auto loaded = io.BinRead(is, component); | ^~~~~~ -[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_sse2.c -[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/adler32_ssse3.c -[ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_ssse3.c -[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Locale.cpp -[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MD5.cpp -[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_pclmulqdq.c -[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -mssse3 -msse4.2 -mpclmul -mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/crc32_vpclmulqdq.c -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_exponential.c -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here - 47 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_fileparser.c -[ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o -MF CMakeFiles/zlibstatic.dir/gzlib.c.o.d -o CMakeFiles/zlibstatic.dir/gzlib.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzlib.c -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gamma.c -[ 20%] Linking CXX static library libsequence.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake -[ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_gencode.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 -[ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o -MF CMakeFiles/zlibstatic.dir/gzread.c.o.d -o CMakeFiles/zlibstatic.dir/gzread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/gzread.c -[ 21%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/ManagedStatic.cpp -[ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -MF CMakeFiles/zlibstatic.dir/gzwrite.c.o.d -o CMakeFiles/zlibstatic.dir/gzwrite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzwrite.c -/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o -/usr/bin/ranlib libsequence.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_getopts.c -[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -cd 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cmake_link_script CMakeFiles/zlibstatic.dir/link.txt --verbose=1 -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_huffman.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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CMakeFiles/zlibstatic.dir/deflate_medium.c.o CMakeFiles/zlibstatic.dir/deflate_quick.c.o CMakeFiles/zlibstatic.dir/deflate_rle.c.o CMakeFiles/zlibstatic.dir/deflate_slow.c.o CMakeFiles/zlibstatic.dir/deflate_stored.c.o CMakeFiles/zlibstatic.dir/functable.c.o CMakeFiles/zlibstatic.dir/infback.c.o CMakeFiles/zlibstatic.dir/inflate.c.o CMakeFiles/zlibstatic.dir/inftrees.c.o CMakeFiles/zlibstatic.dir/insert_string.c.o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o CMakeFiles/zlibstatic.dir/slide_hash.c.o CMakeFiles/zlibstatic.dir/trees.c.o CMakeFiles/zlibstatic.dir/uncompr.c.o CMakeFiles/zlibstatic.dir/zutil.c.o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o CMakeFiles/zlibstatic.dir/gzlib.c.o CMakeFiles/zlibstatic.dir/gzread.c.o CMakeFiles/zlibstatic.dir/gzwrite.c.o -/usr/bin/ranlib libz.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp -[ 25%] Built target zlibstatic -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" -[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 26%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kstring.c -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_hyperexp.c -/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o -/usr/bin/ranlib libformat.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 26%] Built target format make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:22: +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 179 | if ( ((p) = malloc(size)) == NULL) { \ + | ^~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:71:3: note: in expansion of macro 'ESL_ALLOC' + 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); + | ^~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:21: +/usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here + 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ + | ^~~~~~ +[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/samtools/sam.c +cd 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_vectorops.c +[ 41%] Building C object ext/bwa/CMakeFiles/bwa.dir/utils.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/utils.c.o -MF CMakeFiles/bwa.dir/utils.c.o.d -o CMakeFiles/bwa.dir/utils.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/utils.c -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_json.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_json.c.o -MF CMakeFiles/easel.dir/esl_json.c.o.d -o CMakeFiles/easel.dir/esl_json.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_json.c -[ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_keyhash.c -[ 28%] Built target mimalloc-obj +[ 41%] Building C object ext/bwa/CMakeFiles/bwa.dir/kthread.c.o +cd 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CMakeFiles/bwa.dir/kthread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kthread.c +[ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" -[ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_aux.c +[ 42%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_weibull.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 28%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/samtools/bam_pileup.c +[ 43%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o -MF CMakeFiles/graphio.dir/gfa.cpp.o.d -o CMakeFiles/graphio.dir/gfa.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Regex.cpp -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Signals.cpp -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o -[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_lognormal.c.o -MF CMakeFiles/easel.dir/esl_lognormal.c.o.d -o CMakeFiles/easel.dir/esl_lognormal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_lognormal.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_matrixops.c.o -MF CMakeFiles/easel.dir/esl_matrixops.c.o.d -o CMakeFiles/easel.dir/esl_matrixops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_matrixops.c -[ 30%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o +[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_lpileup.c +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 335 | fread(magic, 1, 4, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 342 | fread(&idx->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 355 | fread(&size, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 358 | fread(&key, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 362 | fread(&p->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 366 | fread(p->list, 16, p->n, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 376 | fread(&index2->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o +[ 45%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SmallVector.cpp -[ 30%] Building C object ext/bwa/CMakeFiles/bwa.dir/kthread.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kthread.c.o -MF CMakeFiles/bwa.dir/kthread.c.o.d -o CMakeFiles/bwa.dir/kthread.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kthread.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mem.c -[ 30%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam.c -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/SourceMgr.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_minimizer.c -[ 30%] Building C object ext/bwa/CMakeFiles/bwa.dir/ksw.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_writer.cpp +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_md.c +[ 45%] Building C object ext/bwa/CMakeFiles/bwa.dir/ksw.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/ksw.c.o -MF CMakeFiles/bwa.dir/ksw.c.o.d -o CMakeFiles/bwa.dir/ksw.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/ksw.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixdchlet.c.o -MF CMakeFiles/easel.dir/esl_mixdchlet.c.o.d -o CMakeFiles/easel.dir/esl_mixdchlet.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixdchlet.c -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.cpp:100: -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] - 94 | mi = ::mallinfo(); - | ~~~~~~~~~~^~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Process.inc:35: -/usr/include/malloc.h:114:24: note: declared here - 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; - | ^~~~~~~~ -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mixgev.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_mpi.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msa.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -cd 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CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msacluster.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile2.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_a2m.c -[ 34%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_workqueue.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_wuss.c +[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/bgzf.c.o -MF CMakeFiles/samtools.dir/bgzf.c.o.d -o CMakeFiles/samtools.dir/bgzf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bgzf.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sse.c +[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx.c +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwt.c.o -MF CMakeFiles/bwa.dir/bwt.c.o.d -o CMakeFiles/bwa.dir/bwt.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt.c -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o -MF CMakeFiles/bwa.dir/bntseq.c.o.d -o CMakeFiles/bwa.dir/bntseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bntseq.c +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwa.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwa.c.o -MF CMakeFiles/bwa.dir/bwa.c.o.d -o CMakeFiles/bwa.dir/bwa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwa.c +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o -MF CMakeFiles/bwa.dir/bwamem.c.o.d -o CMakeFiles/bwa.dir/bwamem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem.c +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o -MF CMakeFiles/bwa.dir/bwamem_pair.c.o.d -o CMakeFiles/bwa.dir/bwamem_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_pair.c +[ 46%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o +[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o -MF CMakeFiles/bwa.dir/bwamem_extra.c.o.d -o CMakeFiles/bwa.dir/bwamem_extra.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_extra.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o -MF CMakeFiles/easel.dir/esl_avx512.c.o.d -o CMakeFiles/easel.dir/esl_avx512.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx512.c +[ 46%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/fastg_writer.cpp +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/faidx.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c +[ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o -MF CMakeFiles/bwa.dir/malloc_wrap.c.o.d -o CMakeFiles/bwa.dir/malloc_wrap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/malloc_wrap.c +[ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/is.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/is.c.o -MF CMakeFiles/bwa.dir/is.c.o.d -o CMakeFiles/bwa.dir/is.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/is.c +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_flush': +/build/reproducible-path/spades-4.0.0+dfsg1/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function '_razf_write': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_close': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_end_flush': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'save_zindex': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | write(fd, &v32, sizeof(uint32_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o +[ 48%] Linking CXX static library libformat.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bedidx.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_sort.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/sam_header.c +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_reheader.c +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/knetfile.c.o -MF CMakeFiles/samtools.dir/knetfile.c.o.d -o CMakeFiles/samtools.dir/knetfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c +[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o +[ 48%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o -MF CMakeFiles/bwa.dir/bwtindex.c.o.d -o CMakeFiles/bwa.dir/bwtindex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtindex.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kprobaln.c +/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o +/usr/bin/ranlib libformat.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 48%] Built target format +[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_neon.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_neon.c.o -MF CMakeFiles/easel.dir/esl_neon.c.o.d -o CMakeFiles/easel.dir/esl_neon.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_neon.c +[ 51%] Building C object ext/bwa/CMakeFiles/bwa.dir/rope.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rope.c.o -MF CMakeFiles/bwa.dir/rope.c.o.d -o CMakeFiles/bwa.dir/rope.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c +[ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_cat.c +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:46: +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'kftp_send_cmd': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:236:9: note: in expansion of macro 'netwrite' + 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); + | ^~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'khttp_connect_file': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:415:9: note: in expansion of macro 'netwrite' + 415 | netwrite(fp->fd, buf, l); + | ^~~~~~~~ +[ 51%] Building C object ext/bwa/CMakeFiles/bwa.dir/rle.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rle.c.o -MF CMakeFiles/bwa.dir/rle.c.o.d -o CMakeFiles/bwa.dir/rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rle.c +[ 51%] Building C object ext/bwa/CMakeFiles/bwa.dir/kstring.c.o +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here + 47 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); + | ^~~~~~ +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kstring.c.o -MF CMakeFiles/bwa.dir/kstring.c.o.d -o CMakeFiles/bwa.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kstring.c +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore_node': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fread(&is_bottom, 1, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 283 | fread(&n, 2, 1, fp); + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 291 | fread(p[i].c, 8, 6, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 292 | fread(q, 2, 1, fp); + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 293 | fread(q + 1, 1, *q, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 312 | fread(&r->max_nodes, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 313 | fread(&r->block_len, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Linking CXX static library libsequence.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/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 +/usr/bin/ranlib libsequence.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 51%] Built target sequence /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In lambda function: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:69:77: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 69 | auto exponent = exp_char >> (dsl::lit_c<'+'> | dsl::lit_c<'-'>) + dsl::digits<>; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringExtras.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:74:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 71 | dsl::position + | ~~~~~~~~~~~~~~~ @@ -2416,8 +2742,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 192 | dsl::p; | ~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringMap.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:216:58: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 212 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2444,22 +2768,88 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:269:41: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 269 | dsl::ascii::alpha >> tab + dsl::until(dsl::newline).or_eof() | | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringRef.cpp -[ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_import.c -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/StringSaver.cpp -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o 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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 51%] Built target mimalloc-obj +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger_impl.cpp +[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o +cd 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-o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers_thread.cpp +[ 52%] Built target easel +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion 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directory '/build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/build.c +[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 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CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/heatmap.c +[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o +[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdutils.c +[ 57%] Linking C static library libsamtools.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: In instantiation of 'gfa::grammar::cigar_string::cigarop:: [with auto:48 = lexy::lexeme; uint32_t = unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:19:60: required by substitution of 'template using lexy::_detect_callback_for = decltype (declval()((declval)()...)) [with T = lexy::_callback >; Args = {unsigned int&, lexy::lexeme&&}]' 19 | using _detect_callback_for = decltype(LEXY_DECLVAL(const T)(LEXY_DECLVAL(Args)...)); @@ -2502,72 +2892,114 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:151:37: warning: conversion from 'uint32_t' {aka 'unsigned int'} to 'unsigned int:24' may change value [-Wconversion] 151 | return gfa::cigarop{cnt, lexeme[0]}; | ^~~ -[ 35%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwa.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwa.c.o -MF CMakeFiles/bwa.dir/bwa.c.o.d -o CMakeFiles/bwa.dir/bwa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwa.c -[ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_psiblast.c -[ 35%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_phylip.c -[ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection 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-O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o -MF CMakeFiles/bwa.dir/bwamem.c.o.d -o CMakeFiles/bwa.dir/bwamem.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem.c -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/TimeProfiler.cpp -[ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Twine.cpp -[ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Unicode.cpp -[ 37%] Linking CXX static library libcoverage_model.a -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_selex.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/WithColor.cpp -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLParser.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -cd 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CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_stockholm.c -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/YAMLTraits.cpp -[ 37%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msashuffle.c -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 335 | fread(magic, 1, 4, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 342 | fread(&idx->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | fread(&size, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 358 | fread(&key, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 362 | fread(&p->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 366 | fread(p->list, 16, p->n, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 376 | fread(&index2->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -/usr/bin/ranlib libcoverage_model.a +[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/logsum.c +[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/modelstats.c +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/mpisupport.c +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/seqmodel.c +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_bg.c +/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/bgzf.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/knetfile.c.o CMakeFiles/samtools.dir/bam_cat.c.o +/usr/bin/ranlib libsamtools.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 37%] Built target coverage_model -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmxchk.c +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmcache.c +make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o +cd 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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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-4.0.0+dfsg1/ext/src/hmmer/src/p7_scoredata.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o -MF CMakeFiles/samio.dir/bam_parser.cpp.o.d -o CMakeFiles/samio.dir/bam_parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/bam_parser.cpp +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 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+[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/hmmpgmd2msa.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/fm_general.c +[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_ssv.c +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/decoding.c +[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/fwdback.c +[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/io.c +[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer 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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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/ssvfilter.c +[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/msvfilter.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/null2.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/optacc.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/vitfilter.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_oprofile.c +[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_omx.c +[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/mpi.c In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:108:13: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' @@ -2579,288 +3011,69 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ -[ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_os_ostream.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regcomp.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/raw_ostream.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_paml.c -[ 39%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o -MF CMakeFiles/bwa.dir/bwamem_extra.c.o.d -o CMakeFiles/bwa.dir/bwamem_extra.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwamem_extra.c -[ 40%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -[ 40%] Building C object ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regerror.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_random.c -[ 41%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regexec.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rand64.c.o -MF CMakeFiles/easel.dir/esl_rand64.c.o.d -o CMakeFiles/easel.dir/esl_rand64.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rand64.c -[ 41%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -[ 41%] Building C object ext/bwa/CMakeFiles/bwa.dir/is.c.o -cd 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regfree.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/is.c.o -MF CMakeFiles/bwa.dir/is.c.o.d -o CMakeFiles/bwa.dir/is.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/is.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_randomseq.c -[ 41%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/regstrlcpy.c -[ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ratematrix.c -[ 42%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/samtools/bam_pileup.c -[ 42%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_lpileup.c -[ 42%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/bwtindex.c.o -MF CMakeFiles/bwa.dir/bwtindex.c.o.d -o CMakeFiles/bwa.dir/bwtindex.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtindex.c -[ 42%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_md.c -[ 42%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_recorder.c -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o -[ 43%] Building C object ext/bwa/CMakeFiles/bwa.dir/rope.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rope.c.o -MF CMakeFiles/bwa.dir/rope.c.o.d -o CMakeFiles/bwa.dir/rope.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_red_black.c.o -MF CMakeFiles/easel.dir/esl_red_black.c.o.d -o CMakeFiles/easel.dir/esl_red_black.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_red_black.c -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/bgzf.c.o -MF CMakeFiles/samtools.dir/bgzf.c.o.d -o CMakeFiles/samtools.dir/bgzf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bgzf.c -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore_node': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 282 | fread(&is_bottom, 1, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 283 | fread(&n, 2, 1, fp); - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 291 | fread(p[i].c, 8, 6, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 292 | fread(q, 2, 1, fp); - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 293 | fread(q + 1, 1, *q, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c: In function 'rope_restore': -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 312 | fread(&r->max_nodes, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 313 | fread(&r->block_len, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_regexp.c -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_rootfinder.c -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/faidx.c -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_flush': -/build/reproducible-path/spades-4.0.0+dfsg1/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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function '_razf_write': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_close': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'razf_end_flush': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c: In function 'save_zindex': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | write(fd, &v32, sizeof(uint32_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c -[ 43%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sq.c -[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bedidx.c -[ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio.c -[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_sort.c -[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/sam_header.c -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:22: -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:179:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 179 | if ( ((p) = malloc(size)) == NULL) { \ - | ^~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c:71:3: note: in expansion of macro 'ESL_ALLOC' - 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); - | ^~~~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.h:21: -/usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here - 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ - | ^~~~~~ -[ 45%] Building C object ext/bwa/CMakeFiles/bwa.dir/rle.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rle.c.o -MF CMakeFiles/bwa.dir/rle.c.o.d -o CMakeFiles/bwa.dir/rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rle.c -[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_reheader.c -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ascii.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sqio_ncbi.c -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_ssi.c -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/kprobaln.c -[ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stack.c -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/knetfile.c.o -MF CMakeFiles/samtools.dir/knetfile.c.o.d -o CMakeFiles/samtools.dir/knetfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:46: -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'kftp_send_cmd': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:236:9: note: in expansion of macro 'netwrite' - 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); - | ^~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c: In function 'khttp_connect_file': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/knetfile.c:415:9: note: in expansion of macro 'netwrite' - 415 | netwrite(fp->fd, buf, l); - | ^~~~~~~~ -[ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools/bam_cat.c -[ 47%] Building C object ext/bwa/CMakeFiles/bwa.dir/kstring.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/kstring.c.o -MF CMakeFiles/bwa.dir/kstring.c.o.d -o CMakeFiles/bwa.dir/kstring.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kstring.c -[ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stats.c -[ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_stopwatch.c -[ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_subcmd.c.o -MF CMakeFiles/easel.dir/esl_subcmd.c.o.d -o CMakeFiles/easel.dir/esl_subcmd.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_subcmd.c -[ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common 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cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 48%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_vectorops.c -[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_weibull.c -[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/path_helper.cpp -[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_sse.c -[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_avx.c -[ 50%] Linking C static library libsamtools.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 -[ 50%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx512.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_neon.c.o -MF CMakeFiles/easel.dir/esl_neon.c.o.d -o CMakeFiles/easel.dir/esl_neon.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_neon.c -[ 51%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/temporary.cpp -[ 51%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_writer.cpp -[ 51%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/fastg_writer.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/glob.cpp -[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger_impl.cpp -/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/bgzf.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/knetfile.c.o CMakeFiles/samtools.dir/bam_cat.c.o -/usr/bin/ranlib libsamtools.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o -MF CMakeFiles/utils.dir/logger/log_writers.cpp.o.d -o CMakeFiles/utils.dir/logger/log_writers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers.cpp -[ 52%] Built target samtools -make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 52%] Building CXX object common/io/sam/CMakeFiles/samio.dir/read.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/read.cpp.o -MF CMakeFiles/samio.dir/read.cpp.o.d -o CMakeFiles/samio.dir/read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/read.cpp -[ 52%] Building CXX object common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o -MF CMakeFiles/samio.dir/sam_reader.cpp.o.d -o CMakeFiles/samio.dir/sam_reader.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/sam_reader.cpp -[ 53%] Linking C static library libbwa.a +[ 68%] Linking CXX static library libllvm-support.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 +[ 69%] Linking C static library libbwa.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -P CMakeFiles/bwa.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/bwa.dir/link.txt --verbose=1 -[ 53%] Building CXX object common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o -MF CMakeFiles/samio.dir/bam_parser.cpp.o.d -o CMakeFiles/samio.dir/bam_parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam/bam_parser.cpp +/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" +/usr/bin/ranlib libllvm-support.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 69%] Built target llvm-support /usr/bin/ar qc libbwa.a CMakeFiles/bwa.dir/utils.c.o CMakeFiles/bwa.dir/kthread.c.o CMakeFiles/bwa.dir/ksw.c.o CMakeFiles/bwa.dir/bwt.c.o CMakeFiles/bwa.dir/bntseq.c.o CMakeFiles/bwa.dir/bwa.c.o CMakeFiles/bwa.dir/bwamem.c.o CMakeFiles/bwa.dir/bwamem_pair.c.o CMakeFiles/bwa.dir/bwamem_extra.c.o CMakeFiles/bwa.dir/malloc_wrap.c.o CMakeFiles/bwa.dir/is.c.o CMakeFiles/bwa.dir/bwtindex.c.o CMakeFiles/bwa.dir/rope.c.o CMakeFiles/bwa.dir/rle.c.o CMakeFiles/bwa.dir/kstring.c.o /usr/bin/ranlib libbwa.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 53%] Built target bwa +[ 69%] Built target bwa make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/spades-bwa.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 53%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -MF CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o.d -o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/log_writers_thread.cpp -[ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o +[ 69%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o -MF CMakeFiles/spades-bwa.dir/main.c.o.d -o CMakeFiles/spades-bwa.dir/main.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/main.c -[ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o +[ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o +[ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o +[ 70%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.c.o -MF CMakeFiles/spades-bwa.dir/fastmap.c.o.d -o CMakeFiles/spades-bwa.dir/fastmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/fastmap.c -[ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/pemerge.c.o -MF CMakeFiles/spades-bwa.dir/pemerge.c.o.d -o CMakeFiles/spades-bwa.dir/pemerge.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/pemerge.c -[ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/maxk.c.o -MF CMakeFiles/spades-bwa.dir/maxk.c.o.d -o CMakeFiles/spades-bwa.dir/maxk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/maxk.c -[ 53%] Linking C static library libeasel.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 -[ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/kopen.c.o -MF CMakeFiles/spades-bwa.dir/kopen.c.o.d -o CMakeFiles/spades-bwa.dir/kopen.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c -[ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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/build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_main.c +[ 71%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_pair.c +[ 73%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o -MF CMakeFiles/spades-bwa.dir/bwape.c.o.d -o CMakeFiles/spades-bwa.dir/bwape.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwape.c +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c: In function 'bwa_shm_stage': +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] + 29 | ftruncate(shmid, BWA_CTL_SIZE); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | ftruncate(shmid, idx->l_mem); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:548, from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:6: In function 'strncpy', @@ -2881,236 +3094,78 @@ /usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -[ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtgap.c.o -MF CMakeFiles/spades-bwa.dir/bwtgap.c.o.d -o CMakeFiles/spades-bwa.dir/bwtgap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtgap.c -[ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o -[ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.c.o -MF CMakeFiles/spades-bwa.dir/bwaseqio.c.o.d -o CMakeFiles/spades-bwa.dir/bwaseqio.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwaseqio.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bamlite.c.o -MF CMakeFiles/spades-bwa.dir/bamlite.c.o.d -o CMakeFiles/spades-bwa.dir/bamlite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bamlite.c -[ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common 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56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o -[ 56%] Built target easel -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o -MF CMakeFiles/spades-bwa.dir/bwashm.c.o.d -o CMakeFiles/spades-bwa.dir/bwashm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c -make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/build.c -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c: In function 'bwa_shm_stage': -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] - 29 | ftruncate(shmid, BWA_CTL_SIZE); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | ftruncate(shmid, idx->l_mem); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_aux.c -[ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_core.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/cachedb.c -[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -[ 57%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -MF CMakeFiles/hmmer.dir/src/emit.c.o.d -o CMakeFiles/hmmer.dir/src/emit.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/emit.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_chain.c -[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -MF CMakeFiles/hmmer.dir/src/errors.c.o.d -o CMakeFiles/hmmer.dir/src/errors.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/errors.c -[ 57%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o -MF CMakeFiles/spades-bwa.dir/bwt_lite.c.o.d -o CMakeFiles/spades-bwa.dir/bwt_lite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt_lite.c -[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/evalues.c.o -MF CMakeFiles/hmmer.dir/src/evalues.c.o.d -o CMakeFiles/hmmer.dir/src/evalues.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/evalues.c -[ 57%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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/eweight.c.o -MF CMakeFiles/hmmer.dir/src/eweight.c.o.d -o CMakeFiles/hmmer.dir/src/eweight.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/eweight.c -[ 58%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwape.c.o -MF CMakeFiles/spades-bwa.dir/bwape.c.o.d -o CMakeFiles/spades-bwa.dir/bwape.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwape.c -[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback_chk.c -[ 60%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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CMakeFiles/hmmer.dir/src/generic_msv.c.o.d -o CMakeFiles/hmmer.dir/src/generic_msv.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_msv.c -[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o +[ 73%] Linking CXX static library libsamio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -P CMakeFiles/samio.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -MF CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/heatmap.c cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam && /usr/bin/cmake -E cmake_link_script CMakeFiles/samio.dir/link.txt --verbose=1 -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmlogo.c -[ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdmstr.c /usr/bin/ar qc libsamio.a CMakeFiles/samio.dir/read.cpp.o CMakeFiles/samio.dir/sam_reader.cpp.o CMakeFiles/samio.dir/bam_parser.cpp.o /usr/bin/ranlib libsamio.a -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdwrkr.c -[ 63%] Built target samio -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc 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-isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmer.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/logsum.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/mpisupport.c -[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/tracealign.c -[ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmxchk.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmcache.c -[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmwindow.c -[ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_profile.c -[ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src 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-I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/p7_tophits.c -[ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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_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-4.0.0+dfsg1/ext/src/hmmer/src/p7_scoredata.c -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o -MF CMakeFiles/hmmer.dir/src/p7_hit.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hit.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hit.c -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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-cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/hmmpgmd2msa.c -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/fm_alphabet.c -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-bwa.dir/link.d "CMakeFiles/spades-bwa.dir/main.c.o" "CMakeFiles/spades-bwa.dir/fastmap.c.o" "CMakeFiles/spades-bwa.dir/pemerge.c.o" "CMakeFiles/spades-bwa.dir/maxk.c.o" "CMakeFiles/spades-bwa.dir/kopen.c.o" "CMakeFiles/spades-bwa.dir/bwtaln.c.o" "CMakeFiles/spades-bwa.dir/bwtgap.c.o" "CMakeFiles/spades-bwa.dir/bwaseqio.c.o" "CMakeFiles/spades-bwa.dir/bamlite.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o" "CMakeFiles/spades-bwa.dir/bwashm.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o" "CMakeFiles/spades-bwa.dir/bwt_lite.c.o" "CMakeFiles/spades-bwa.dir/bwape.c.o" "CMakeFiles/spades-bwa.dir/bwase.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o" -o ../../bin/spades-bwa libbwa.a ../../_deps/zlib_ng-build/libz.a -lm +[ 73%] Built target samio +[ 73%] Linking CXX static library libcoverage_model.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 69%] Built target spades-bwa -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -[ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/decoding.c -[ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/fwdback.c -[ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/io.c -[ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/ssvfilter.c -[ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/msvfilter.c /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.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 CMakeFiles/utils.dir/logger/log_writers.cpp.o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/null2.c -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/optacc.c -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/stotrace.c -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -cd 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-ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/vitfilter.c -[ 71%] Built target utils +[ 73%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 71%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/id_distributor.cpp -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_omx.c -[ 71%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/components/connected_component.cpp -[ 71%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -[ 73%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/p7_oprofile.c -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/impl_sse/mpi.c -[ 73%] Building CXX object 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common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.cpp -[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/id_distributor.cpp +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o [ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/components/connected_component.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp +[ 74%] Linking C executable ../../bin/spades-bwa +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-bwa.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-bwa.dir/link.d "CMakeFiles/spades-bwa.dir/main.c.o" "CMakeFiles/spades-bwa.dir/fastmap.c.o" "CMakeFiles/spades-bwa.dir/pemerge.c.o" "CMakeFiles/spades-bwa.dir/maxk.c.o" "CMakeFiles/spades-bwa.dir/kopen.c.o" "CMakeFiles/spades-bwa.dir/bwtaln.c.o" "CMakeFiles/spades-bwa.dir/bwtgap.c.o" "CMakeFiles/spades-bwa.dir/bwaseqio.c.o" "CMakeFiles/spades-bwa.dir/bamlite.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o" "CMakeFiles/spades-bwa.dir/bwashm.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o" "CMakeFiles/spades-bwa.dir/bwt_lite.c.o" "CMakeFiles/spades-bwa.dir/bwape.c.o" "CMakeFiles/spades-bwa.dir/bwase.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o" -o ../../bin/spades-bwa libbwa.a ../../_deps/zlib_ng-build/libz.a -lm +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Built target spades-bwa +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:8: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] + 142 | } + | ^ +[ 74%] Linking C static library libhmmer.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/p7_hit.c.o CMakeFiles/hmmer.dir/src/p7_domain.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +/usr/bin/ranlib libhmmer.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Built target hmmer +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +[ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp [ 74%] Linking CXX static library libgraphio.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/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.cpp.o CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o -/usr/bin/ranlib libgraphio.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 74%] Built target graphio In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_info_updater.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:10: @@ -3139,6 +3194,83 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp:21:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 21 | IdHolder edge_id_; | ^~~~~~~~ +cd /build/reproducible-path/spades-4.0.0+dfsg1/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.cpp.o CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o +/usr/bin/ranlib libgraphio.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Built target graphio +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp: In constructor 'hmmer::HMMFile::HMMFile(const std::string&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:53:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 53 | p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:55:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 55 | p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:57:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 57 | p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile.c_str(), errbuf); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp:166:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 166 | pli->Z = pli->domZ = cfg.Z; + | ~~~~^ +[ 74%] Linking CXX static library libhmmercpp.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +/usr/bin/ranlib libhmmercpp.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Built target hmmercpp +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o +[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/mismatch_correction.cpp +[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o +[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp +[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o +[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pair_info_count.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/extract_domains.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/distance_estimation.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/contig_output_stage.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/chromosome_removal.cpp +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o +[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp +[ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/load_graph.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/restricted_edges_filling.cpp +[ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -MF CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o.d -o CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/wastewater_disentangle.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph.cpp +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(graph_pack::GraphPack&, const char*)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp:26:9: warning: unused variable 'code' [-Wunused-variable] + 26 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); + | ^~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp:53:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 53 | if (seqpos2.second - seqpos2.first < model_length / 10) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:11: +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, @@ -3185,13 +3317,17 @@ /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:8: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:142:5: warning: control reaches end of non-void function [-Wreturn-type] - 142 | } - | ^ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] + 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); + | ^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] + 486 | bool u2 = UpdateRight(gap, split_orig, split_res); + | ^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] + 659 | size_t cur_len = end_it - start_it; + | ^~~~~~~ In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]', inlined from 'static void phmap::allocator_traits::deallocate(Alloc&, pointer, size_type) [with Alloc = std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M>]' at /usr/include/parallel_hashmap/phmap_base.h:1487:21, inlined from 'void phmap::priv::Deallocate(Alloc*, void*, size_t) [with long unsigned int Alignment = 8; Alloc = std::allocator > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4210:17, @@ -3220,142 +3356,6 @@ /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ -[ 74%] Linking C static library libhmmer.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/p7_hit.c.o CMakeFiles/hmmer.dir/src/p7_domain.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -/usr/bin/ranlib libhmmer.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 74%] Built target hmmer -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp -[ 74%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp: In constructor 'hmmer::HMMFile::HMMFile(const std::string&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:53:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 53 | p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:55:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 55 | p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:57:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 57 | p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile.c_str(), errbuf); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp:166:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 166 | pli->Z = pli->domZ = cfg.Z; - | ~~~~^ -[ 74%] Linking CXX static library libhmmercpp.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -/usr/bin/ranlib libhmmercpp.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 74%] Built target hmmercpp -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -[ 74%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/mismatch_correction.cpp -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pair_info_count.cpp -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp -[ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/distance_estimation.cpp -[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/contig_output_stage.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src 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/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/chromosome_removal.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/extract_domains.cpp -[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp -[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp -[ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/restricted_edges_filling.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/load_graph.cpp -[ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -MF CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o.d -o CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/wastewater_disentangle.cpp -[ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph.cpp -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(graph_pack::GraphPack&, const char*)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp:26:9: warning: unused variable 'code' [-Wunused-variable] - 26 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); - | ^~~~ -[ 78%] Linking CXX static library libbinary_io.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 -/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o -/usr/bin/ranlib libbinary_io.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 78%] Built target binary_io -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/depend -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain/CMakeFiles/toolchain.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 78%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/parser.cpp -[ 78%] Building CXX object common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o -MF CMakeFiles/toolchain.dir/utils.cpp.o.d -o CMakeFiles/toolchain.dir/utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp -[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_converter.cpp -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_matcher.cpp:53:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 53 | if (seqpos2.second - seqpos2.first < model_length / 10) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:11: -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 329 | while (pref_remove < coverages.size() && coverages[pref_remove] < cov / 2 ) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:485:14: warning: unused variable 'u1' [-Wunused-variable] - 485 | bool u1 = UpdateLeft(gap, split_orig, split_res); - | ^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:486:14: warning: unused variable 'u2' [-Wunused-variable] - 486 | bool u2 = UpdateRight(gap, split_orig, split_res); - | ^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] - 659 | size_t cur_len = end_it - start_it; - | ^~~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:10: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:62:63: required from here - 62 | io::binary::BasicGraphIO().Load(filename, graph); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 31 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:232:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 232 | for (;index != res.first; ++index) { @@ -3364,28 +3364,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp:259:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 259 | if (coords.second + 5000 > path.Length()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here - 43 | bool BinRead(std::istream &is, Graph &graph) override { - | ^~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 44 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here - 47 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_streams.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, @@ -3410,10 +3388,34 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ -[ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/read_converter.cpp -[ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/dataset_readers.cpp +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:11: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here + 30 | bool Load(const std::string &basename, Graph &graph) override { + | ^~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 31 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here + 43 | bool BinRead(std::istream &is, Graph &graph) override { + | ^~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 44 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here + 47 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:12: @@ -3468,7 +3470,7 @@ | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:11: + from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:17: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { @@ -3494,13 +3496,47 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +[ 78%] Linking CXX static library libbinary_io.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 +/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o +/usr/bin/ranlib libbinary_io.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 78%] Built target binary_io +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain/CMakeFiles/toolchain.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make -f common/toolchain/CMakeFiles/toolchain.dir/build.make common/toolchain/CMakeFiles/toolchain.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 78%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o +[ 78%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o +[ 78%] Building CXX object common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/parser.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/toolchain/CMakeFiles/toolchain.dir/utils.cpp.o -MF CMakeFiles/toolchain.dir/utils.cpp.o.d -o CMakeFiles/toolchain.dir/utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/paired_readers.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_converter.cpp +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/binary_streams.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/read_converter.cpp +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o +[ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/dataset_support/dataset_readers.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:17: + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here - 30 | bool Load(const std::string &basename, Graph &graph) override { - | ^~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/toolchain/utils.cpp:62:63: required from here + 62 | io::binary::BasicGraphIO().Load(filename, graph); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ @@ -3522,59 +3558,45 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 79%] Linking CXX static library libtoolchain.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -P CMakeFiles/toolchain.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -E cmake_link_script CMakeFiles/toolchain.dir/link.txt --verbose=1 -/usr/bin/ar qc libtoolchain.a CMakeFiles/toolchain.dir/utils.cpp.o -/usr/bin/ranlib libtoolchain.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 79%] Built target toolchain -[ 80%] Linking CXX static library libinput.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 -[ 80%] Linking CXX static library libassembly_graph.a +[ 79%] Linking CXX static library libassembly_graph.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/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 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 -/usr/bin/ranlib libinput.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 80%] Built target input -make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 80%] Building CXX object common/library/CMakeFiles/library.dir/library.cpp.o -[ 80%] Building CXX object common/library/CMakeFiles/library.dir/library_data.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library.cpp.o -MF CMakeFiles/library.dir/library.cpp.o.d -o CMakeFiles/library.dir/library.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library_data.cpp.o -MF CMakeFiles/library.dir/library_data.cpp.o.d -o CMakeFiles/library.dir/library_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library_data.cpp /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/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 80%] Built target assembly_graph +[ 79%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o +[ 79%] Building CXX object common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o +[ 79%] Building CXX object common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o +[ 79%] Building CXX object common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o +[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o +[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o +[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o +[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o +[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o -MF CMakeFiles/alignment.dir/gap_info.cpp.o.d -o CMakeFiles/alignment.dir/gap_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/gap_info.cpp -[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o -MF CMakeFiles/alignment.dir/bwa_index.cpp.o.d -o CMakeFiles/alignment.dir/bwa_index.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp -[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o -MF CMakeFiles/alignment.dir/long_read_mapper.cpp.o.d -o CMakeFiles/alignment.dir/long_read_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp -[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -MF CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper_notifier.cpp -[ 80%] Building CXX object common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -MF CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o.d -o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_sequence_mapper.cpp -[ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -[ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -[ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -MF CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o.d -o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/g_aligner.cpp +[ 80%] Linking CXX static library libtoolchain.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -P CMakeFiles/toolchain.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -E cmake_link_script CMakeFiles/toolchain.dir/link.txt --verbose=1 +/usr/bin/ar qc libtoolchain.a CMakeFiles/toolchain.dir/utils.cpp.o +/usr/bin/ranlib libtoolchain.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 80%] Built target toolchain +[ 81%] Linking CXX static library libinput.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.hpp:10, @@ -3600,6 +3622,20 @@ | | | long long int | %ld +/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 +/usr/bin/ranlib libinput.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 81%] Built target input +make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 81%] Building CXX object common/library/CMakeFiles/library.dir/library.cpp.o +[ 81%] Building CXX object common/library/CMakeFiles/library.dir/library_data.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library.cpp.o -MF CMakeFiles/library.dir/library.cpp.o.d -o CMakeFiles/library.dir/library.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/library/CMakeFiles/library.dir/library_data.cpp.o -MF CMakeFiles/library.dir/library_data.cpp.o.d -o CMakeFiles/library.dir/library_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library/library_data.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp:15, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'Sequence debruijn_graph::MergeSequences(const Graph&, const std::vector&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]': @@ -3632,10 +3668,10 @@ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 81%] Building CXX object common/configs/CMakeFiles/configs.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/config_struct.cpp.o -MF CMakeFiles/configs.dir/config_struct.cpp.o.d -o CMakeFiles/configs.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/config_struct.cpp +[ 82%] Building CXX object common/configs/CMakeFiles/configs.dir/config_struct.cpp.o [ 82%] Building CXX object common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o -MF CMakeFiles/configs.dir/pe_config_struct.cpp.o.d -o CMakeFiles/configs.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/pe_config_struct.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/configs/CMakeFiles/configs.dir/config_struct.cpp.o -MF CMakeFiles/configs.dir/config_struct.cpp.o.d -o CMakeFiles/configs.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs/config_struct.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, @@ -3740,12 +3776,12 @@ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 82%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -[ 82%] Building CXX object common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -MF CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d -o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaff_supplementary.cpp +[ 84%] Building CXX object common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o +[ 84%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o [ 84%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/genome_consistance_checker.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -MF CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d -o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaff_supplementary.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, @@ -3777,9 +3813,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ -[ 84%] Linking CXX static library libconfigs.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -P CMakeFiles/configs.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -E cmake_link_script CMakeFiles/configs.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:21: /build/reproducible-path/spades-4.0.0+dfsg1/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::const_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:633:18: required from here @@ -3788,50 +3821,9 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:674:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 674 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/bin/ar qc libconfigs.a CMakeFiles/configs.dir/config_struct.cpp.o CMakeFiles/configs.dir/pe_config_struct.cpp.o -/usr/bin/ranlib libconfigs.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 84%] Built target configs -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend 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CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launch_support.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/extenders_logic.cpp -[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include 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CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp -[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include 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common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:36:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 36 | if (sum < absolute_weight_threshold_) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 84%] Linking CXX static library libconfigs.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -P CMakeFiles/configs.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs && /usr/bin/cmake -E cmake_link_script CMakeFiles/configs.dir/link.txt --verbose=1 In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, @@ -3874,6 +3866,46 @@ /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ +/usr/bin/ar qc libconfigs.a CMakeFiles/configs.dir/config_struct.cpp.o CMakeFiles/configs.dir/pe_config_struct.cpp.o +/usr/bin/ranlib libconfigs.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 84%] Built target configs +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd 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common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_detector.cpp +[ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o +[ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o +[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/gap_analyzer.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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-o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_traverser.cpp +[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp +[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o +[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/overlap_remover.cpp +[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launch_support.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp +[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/extenders_logic.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:118:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 118 | if (iter->second < min_read_count_) { @@ -3882,6 +3914,13 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp:124:12: warning: variable 'pin' set but not used [-Wunused-but-set-variable] 124 | EdgeId pin = path[path.Size() - 2]; | ^~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:36:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 36 | if (sum < absolute_weight_threshold_) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Linking CXX static library libspades-stages.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, @@ -3911,9 +3950,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 86%] Linking CXX static library libspades-stages.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/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" "CMakeFiles/spades-stages.dir/wastewater_disentangle.cpp.o" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' @@ -3931,14 +3967,14 @@ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -[ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/weighted_distance_estimation.cpp +[ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/smoothing_distance_estimation.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/weighted_distance_estimation.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/smoothing_distance_estimation.cpp +[ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -MF CMakeFiles/paired_info.dir/paired_info_utils.cpp.o.d -o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_utils.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:18, @@ -3973,27 +4009,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:31:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 31 | size_t min_dist, | ~~~~~~~^~~~~~~~ -[ 86%] Linking CXX static library libpath_extend.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/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/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -/usr/bin/ranlib libpath_extend.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 86%] Built target path_extend -make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack_helpers.cpp -[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -MF CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o.d -o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/sequence_mapper_gp_api.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, @@ -4038,6 +4053,30 @@ /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ +[ 86%] Linking CXX static library libpath_extend.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/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/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +/usr/bin/ranlib libpath_extend.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 86%] Built target path_extend +make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o +[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o +[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp +[ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack_helpers.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -MF CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o.d -o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/sequence_mapper_gp_api.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp +[ 87%] Linking CXX static library libpaired_info.a +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/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]': @@ -4065,6 +4104,10 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +/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 CMakeFiles/paired_info.dir/paired_info_utils.cpp.o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o +/usr/bin/ranlib libpaired_info.a +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 87%] Built target paired_info In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here @@ -4073,13 +4116,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ -[ 87%] Linking CXX static library libpaired_info.a -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake -cd /build/reproducible-path/spades-4.0.0+dfsg1/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 CMakeFiles/paired_info.dir/paired_info_utils.cpp.o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o -/usr/bin/ranlib libpaired_info.a -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 87%] Built target paired_info [ 87%] Linking CXX static library libpipeline.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 @@ -4094,63 +4130,49 @@ make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -[ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o -[ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -[ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o -[ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o +[ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o +[ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o +[ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o +[ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/read_conversion.cpp +[ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o +[ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o +[ 90%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o +[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o +[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/construction.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/read_conversion.cpp -[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/err_helper_table.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/config_struct.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp +[ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/subcluster.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/ss_edge_split.cpp -[ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o +[ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/err_helper_table.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/subcluster.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -[ 92%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_helpers.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -[ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -[ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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-I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT 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-I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/gamma_poisson_model.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/normal_quality_model.cpp -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:33:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 33 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) - | ~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:35:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 35 | num_flows = measurements.size(); - | ~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:53:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] - 53 | unsigned int prefix_size = master_read.sequence.size(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:299:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 299 | int backward_idx = seq.size()-1; - | ~~~~~~~~~~^~ +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_metrics.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/quality_thresholds_estimator.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hamcluster_1.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/normal_quality_model.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/gamma_poisson_model.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:92:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 92 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); @@ -4178,6 +4200,20 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:521:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 521 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:33:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 33 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) + | ~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:35:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 35 | num_flows = measurements.size(); + | ~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:53:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] + 53 | unsigned int prefix_size = master_read.sequence.size(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:299:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 299 | int backward_idx = seq.size()-1; + | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/hkmer.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:9: @@ -4564,95 +4600,125 @@ make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target common_modules make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend +make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend +make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/depend +make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/depend +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" +make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" -make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/depend +make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" +make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" -make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" -make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/depend -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" -make 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gfa-split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build -[ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -[ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/depend -[ 92%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 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-I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/positional_read.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hammer_tools.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/interesting_pos_processor.cpp -[ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build -[ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -[ 95%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -[ 95%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 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projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -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 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -MF CMakeFiles/spades-gmapper.dir/gmapper.cpp.o.d -o CMakeFiles/spades-gmapper.dir/gmapper.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp -[ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=524288UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -MF CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/gbuilder.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gbuilder.cpp +[ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +[ 95%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +[ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +[ 95%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o +[ 96%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp +[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/main.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/interesting_pos_processor.cpp +[ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o +[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp +[ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o [ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/cds_subgraphs/profile_storage.cpp -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hammer_tools.cpp +[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o +[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +[ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/main.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng 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-fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_data.cpp [ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o +[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o -MF 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -MF CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o.d -o CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gfa_split.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/expander.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -MF CMakeFiles/spades-kmercount.dir/kmercount.cpp.o.d -o CMakeFiles/spades-kmercount.dir/kmercount.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp -[ 98%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/main.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=4194304UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 -DBLAZE_USE_FUNCTION_TRACES=0 -DBLAZE_USE_VECTORIZATION=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/config_struct_hammer.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 162 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { @@ -4707,22 +4773,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp:73:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 73 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ -make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/read_filter.cpp -make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmer_estimating.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:134:19: warning: unused variable 'mode' [-Wunused-variable] 134 | pipeline_type mode = cfg::get().mode; @@ -4731,16 +4781,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp:236:46: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 236 | graph_pack::GraphPack conj_gp(cfg::get().K, | ~~~~~~~~~~~^ -make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/depend -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gfa-split.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build -make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -MF CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o.d -o CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gfa_split.cpp -[ 98%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/gsimplifier.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:25: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp: In function 'std::string debruijn_graph::gap_closing::SPOAConsensus(const std::vector >&, const debruijn_graph::config::pacbio_processor&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:329:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] @@ -4757,10 +4797,18 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:659:16: warning: unused variable 'cur_len' [-Wunused-variable] 659 | size_t cur_len = end_it - start_it; | ^~~~~~~ -[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/series_analysis.cpp -[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/mts/contig_abundance.cpp +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gsimplifier.cpp:8: +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp: In function 'void debruijn::simplification::Simplify(graph_pack::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] + 103 | const bool using_edge_qual = edge_qual.IsAttached(); + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp:344:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 344 | for (uint32_t j=0; j::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here @@ -4922,23 +4970,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp:344:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 344 | for (uint32_t j=0; j&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] - 103 | const bool using_edge_qual = edge_qual.IsAttached(); - | ^~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/spades-corrector-core -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-corrector-core.dir/link.d "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 98%] Built target spades-corrector-core In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:9: @@ -5033,6 +5064,8 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +[ 98%] Linking CXX executable ../../bin/spades-corrector-core +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' @@ -5096,6 +5129,11 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-corrector-core.dir/link.d "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 98%] Built target spades-corrector-core +[ 98%] Linking CXX executable ../../bin/spades-core +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm @@ -5103,8 +5141,9 @@ [ 98%] Built target spades-convert-bin-to-fasta [ 98%] Linking CXX executable ../../bin/spades-kmer-estimating cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 -[ 98%] Linking CXX executable ../../bin/spades-core -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-core.dir/link.d "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 98%] Built target spades-core /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-kmer-estimating.dir/link.d "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-kmer-estimating @@ -5113,24 +5152,21 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-hammer.dir/link.d "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/kmer_index/libmph_index.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/modules/path_extend/libpath_extend.a -lssw ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-hammer -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-core.dir/link.d "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 98%] Built target spades-core [ 98%] Linking CXX executable ../../bin/spades-gfa-split cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gfa-split.dir/link.txt --verbose=1 +[ 98%] Linking CXX executable ../../bin/spades-read-filter +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gfa-split.dir/link.d "CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gfa-split ../../common/io/graph/libgraphio.a ../../common/toolchain/libtoolchain.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/binary/libbinary_io.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-gfa-split +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm +make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 98%] Built target spades-read-filter [100%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /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-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-kmercount.dir/link.d "CMakeFiles/spades-kmercount.dir/kmercount.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/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-kmercount -[100%] Linking CXX executable ../../bin/spades-read-filter -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm -make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[100%] Built target spades-read-filter [100%] Linking CXX executable ../../bin/spades-gmapper cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /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-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file,CMakeFiles/spades-gmapper.dir/link.d "CMakeFiles/spades-gmapper.dir/gmapper.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 ../../common/hmm/libhmmercpp.a ../../ext/hmmer/libhmmer.a -lspoa ../../ext/easel/libeasel.a ../../ext/lexy/src/liblexy_file.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm @@ -5158,31 +5194,31 @@ make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" +make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/DependInfo.cmake "--color=" +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" @@ -5190,318 +5226,324 @@ cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" -Dependencies file "ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.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-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". +Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". -Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.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-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target lexy_file -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Dependencies file "common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src/CMakeFiles/lexy_file.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target mimalloc-obj +Consolidate compiler generated dependencies of target edlib Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +Dependencies file "common/kmer_index/CMakeFiles/mph_index.dir/kmer_mph/kmer_buckets.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target lexy_file +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target format +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target version +Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target mph_index +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target edlib +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target version Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target gqf +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target gqf Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target coverage_model +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/cpu_features.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid_comb.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target mph_index +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_fold.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/lexy/src/CMakeFiles/lexy_file.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_fast.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_huff.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_medium.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_quick.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target format Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +Consolidate compiler generated dependencies of target teamcity_gtest make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_slow.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_stored.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/lexy/src/CMakeFiles/lexy_file.dir/build'. +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 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"/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f 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Consolidate compiler generated dependencies of target binary_io -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/inftrees.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/uncompr.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +Dependencies file "_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 2%] Built target version +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 2%] Built target edlib make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/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/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 2%] Built target lexy_file Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 2%] Built target gqf -Consolidate compiler generated dependencies of target zlibstatic Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -[ 4%] Built target teamcity_gtest Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 4%] Built target mph_index -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 6%] Built target format Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +[ 0%] Built target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 9%] Built target mimalloc-obj -[ 9%] Built target coverage_model -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +[ 2%] Built target version +[ 2%] Built target lexy_file +[ 4%] Built target format +[ 6%] Built target mimalloc-obj +[ 6%] Built target mph_index +Consolidate compiler generated dependencies of target zlibstatic make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build +[ 6%] Built target gqf make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +[ 9%] Built target teamcity_gtest +[ 9%] Built target coverage_model [ 11%] Built target binary_io +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target sequence Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -[ 29%] Built target zlibstatic -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "common/utils/CMakeFiles/utils.dir/logger/log_writers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build Dependencies file "common/utils/CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target sequence +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build +[ 29%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +Consolidate compiler generated dependencies of target utils make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +Consolidate compiler generated dependencies of target llvm-support make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". +[ 29%] Built target sequence Dependencies file "ext/bwa/CMakeFiles/bwa.dir/bwa.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/compiler_depend.internal". +Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". 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Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". -Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/faidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/knetfile.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Dependencies file "common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/compiler_depend.internal". +[ 31%] Built target utils Consolidate compiler generated dependencies of target bwa make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build +Consolidate compiler generated dependencies of target samtools make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target samtools -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build Consolidate compiler generated dependencies of target graphio -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build -[ 31%] Built target utils make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/graph/CMakeFiles/graphio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 38%] Built target bwa -[ 47%] Built target samtools +[ 52%] Built target llvm-support +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +[ 59%] Built target bwa +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" +[ 68%] Built target samtools make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" -Consolidate compiler generated dependencies of target llvm-support -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 50%] Built target graphio -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build +[ 70%] Built target graphio +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/sam/CMakeFiles/samio.dir/bam_parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/sam/CMakeFiles/samio.dir/read.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". Dependencies file "common/io/sam/CMakeFiles/samio.dir/sam_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target samio +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/sam/CMakeFiles/samio.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 70%] 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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" +Consolidate compiler generated dependencies of target assembly_graph +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build [ 70%] Built target samio make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". -Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/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 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"/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". @@ -5509,81 +5551,84 @@ Dependencies file "common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 72%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" -[ 77%] Built target input -make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" +Consolidate compiler generated dependencies of target input +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build Dependencies file "common/alignment/CMakeFiles/alignment.dir/bwa_index.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Dependencies file "common/alignment/CMakeFiles/alignment.dir/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". Dependencies file "common/alignment/CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/compiler_depend.internal". +[ 77%] Built target input +make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" +Consolidate compiler generated dependencies of target alignment +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build Dependencies file "common/library/CMakeFiles/library.dir/library.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/compiler_depend.internal". Dependencies file "common/library/CMakeFiles/library.dir/library_data.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/compiler_depend.internal". +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target library make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/library/CMakeFiles/library.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target alignment -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 77%] Built target library -make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build +[ 79%] Built target alignment +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" +[ 79%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +Dependencies file "common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". +Dependencies file "common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/configs/CMakeFiles/configs.dir/config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/compiler_depend.internal". Dependencies file "common/configs/CMakeFiles/configs.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/compiler_depend.internal". -[ 79%] Built target alignment -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" +Consolidate compiler 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Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/configs/CMakeFiles/configs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Dependencies file "common/modules/CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -[ 81%] Built target configs +[ 84%] Built target modules +[ 84%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make 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Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". @@ -5595,28 +5640,19 @@ 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-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". 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"common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target path_extend Consolidate compiler generated dependencies of target paired_info make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target path_extend -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/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 -[ 86%] Built target paired_info make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 86%] Built target paired_info [ 90%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' @@ -5665,30 +5701,30 @@ make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_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/test_utils.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -MF CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/paired_info_test.cpp -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -MF CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/paired_info_test.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/histogram_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/overlap_analysis_test.cpp -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -MF CMakeFiles/debruijn_test.dir/test_utils.cpp.o.d -o CMakeFiles/debruijn_test.dir/test_utils.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -MF CMakeFiles/debruijn_test.dir/construction_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/construction_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/path_extend_test.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/overlap_removal_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/path_extend_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o -MF CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o.d -o CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DLEXY_HAS_UNICODE_DATABASE=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/../include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++20 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test.cpp @@ -5699,6 +5735,50 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:73:21: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 73 | Graph gfa_graph(K); | ^ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:8: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:142:26: required from here + 142 | helper.DeleteLink(vertex, out_edge); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] + 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); + | ^~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:23:12: warning: unused variable 'read_count' [-Wunused-variable] + 23 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, + | ^~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::Point&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:30:12: warning: unused variable 'read_count' [-Wunused-variable] + 30 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, + | ^~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadGraph(const std::string&, debruijn_graph::Graph&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:69:26: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 69 | VertexId new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), vid, conj_vid); + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:127:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 127 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:192:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] + 192 | int read_count = fscanf(file, "%zu\n", &pos_count); + | ^~~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:8: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' + 508 | queue_.pop(); + | ~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' + 252 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:85:57: required from here + 85 | for (auto it = g.SmartVertexBegin(); !it.IsEnd(); ++it) { + | ^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] + 142 | bool res = set_.erase(queue_.top()); + | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, @@ -5733,69 +5813,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:8: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:142:26: required from here - 142 | helper.DeleteLink(vertex, out_edge); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:118:14: warning: unused variable 'res' [-Wunused-variable] - 118 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); - | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:8: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' - 508 | queue_.pop(); - | ~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' - 252 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_core_test.cpp:85:57: required from here - 85 | for (auto it = g.SmartVertexBegin(); !it.IsEnd(); ++it) { - | ^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] - 142 | bool res = set_.erase(queue_.top()); - | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:12: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here - 47 | void LoadImpl(BinIStream &str, Graph &graph) override { - | ^~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); - | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:11: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here - 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ^~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] - 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { - | ~~~~~~~^~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:23:12: warning: unused variable 'read_count' [-Wunused-variable] - 23 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, - | ^~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::Point&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:30:12: warning: unused variable 'read_count' [-Wunused-variable] - 30 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, - | ^~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadGraph(const std::string&, debruijn_graph::Graph&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:69:26: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 69 | VertexId new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), vid, conj_vid); - | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:127:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 127 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); - | ^~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.cpp:192:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] - 192 | int read_count = fscanf(file, "%zu\n", &pos_count); - | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp: In member function 'size_t debruijn_graph::DeBruijnGraph::link_length(VertexId, EdgeId, EdgeId) const': @@ -5829,10 +5846,25 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:190:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 190 | gap_cfg.penalty_ratio = 0.1; | ^~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp: In function 'void CheckIndex(const std::vector >&, const std::filesystem::__cxx11::path&, size_t)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp:68:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] - 68 | graph_pack::GraphPack gp(k, tmpdir, 0); - | ^ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:12: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here + 47 | void LoadImpl(BinIStream &str, Graph &graph) override { + | ^~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); + | ^~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:11: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:10: required from here + 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ^~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/kmer_mapper.hpp:148:28: warning: unused parameter 'new_edge' [-Wunused-parameter] + 148 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { + | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, @@ -5882,6 +5914,10 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp: In function 'void CheckIndex(const std::vector >&, const std::filesystem::__cxx11::path&, size_t)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/construction_test.cpp:68:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] + 68 | graph_pack::GraphPack gp(k, tmpdir, 0); + | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp: In function 'void test_utils::AssertGraph(size_t, const std::vector >&, const std::vector >&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:131:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 131 | Graph g(k); @@ -5911,6 +5947,26 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] 142 | bool res = set_.erase(queue_.top()); | ^~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:10: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' + 508 | queue_.pop(); + | ~~~~~~~~~~^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' + 252 | ++inner_it_; + | ^~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:122:55: required from here + 122 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { + | ^~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] + 142 | bool res = set_.erase(queue_.top()); + | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); @@ -6001,37 +6057,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:55:16: warning: unused variable 'cnt' [-Wunused-variable] 55 | size_t cnt = border_.erase(v); | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:13, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph.hpp:12, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.hpp:10, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/sequence_mapper.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:10: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' - 508 | queue_.pop(); - | ~~~~~~~~~~^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/graph_iterators.hpp:252:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' - 252 | ++inner_it_; - | ^~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:122:55: required from here - 122 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { - | ^~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:142:14: warning: unused variable 'res' [-Wunused-variable] - 142 | bool res = set_.erase(queue_.top()); - | ^~~ -In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' - 721 | auto interacting_edges = RetainIndependentBulges(bulges); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here - 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { - | ^~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] - 582 | size_t total_cnt = bulges.size(); - | ^~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_visualizer.hpp:13, @@ -6061,6 +6086,41 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +In file included from /usr/include/c++/14/string:51, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/perf/perfcounter.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:14, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:10: +In static member function 'static void std::__copy_move::__assign_one(_Tp*, _Up*) [with _Tp = long unsigned int; _Up = const long unsigned int]', + inlined from 'static constexpr _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const long unsigned int; _Up = long unsigned int; bool _IsMove = false]' at /usr/include/c++/14/bits/stl_algobase.h:455:20, + inlined from 'constexpr _OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from 'constexpr _OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from 'constexpr _OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from 'constexpr _OI std::copy(_II, _II, _OI) [with _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from 'constexpr _ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*; _Tp = long unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const long unsigned int*; _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1697:33, + inlined from 'constexpr std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:682:21, + inlined from 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:133:51: +/usr/include/c++/14/bits/stl_algobase.h:413:17: warning: 'split_link' may be used uninitialized [-Wmaybe-uninitialized] + 413 | { *__to = *__from; } + | ~~~~~~^~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp: In function 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)': +/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:124:20: note: 'split_link' was declared here + 124 | LinkId split_link; + | ^~~~~~~~~~ +In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:721:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' + 721 | auto interacting_edges = RetainIndependentBulges(bulges); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:678:12: required from here + 678 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { + | ^~~ +/build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/bulge_remover.hpp:582:16: warning: unused variable 'total_cnt' [-Wunused-variable] + 582 | size_t total_cnt = bulges.size(); + | ^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:508:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 508 | queue_.pop(); @@ -6095,30 +6155,6 @@ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:50:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 50 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:51, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/perf/perfcounter.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:14, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/core/construction_helper.hpp:10: -In static member function 'static void std::__copy_move::__assign_one(_Tp*, _Up*) [with _Tp = long unsigned int; _Up = const long unsigned int]', - inlined from 'static constexpr _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const long unsigned int; _Up = long unsigned int; bool _IsMove = false]' at /usr/include/c++/14/bits/stl_algobase.h:455:20, - inlined from 'constexpr _OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from 'constexpr _OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from 'constexpr _OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from 'constexpr _OI std::copy(_II, _II, _OI) [with _II = const long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from 'constexpr _ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const long unsigned int*; _ForwardIterator = long unsigned int*; _Tp = long unsigned int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'constexpr void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const long unsigned int*; _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1697:33, - inlined from 'constexpr std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:682:21, - inlined from 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:133:51: -/usr/include/c++/14/bits/stl_algobase.h:413:17: warning: 'split_link' may be used uninitialized [-Wmaybe-uninitialized] - 413 | { *__to = *__from; } - | ~~~~~~^~~~~~~~~ -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp: In function 'void PerformSplits(debruijn_graph::Graph&, std::ifstream&, const IdMapper&)': -/build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/v_overlaps.cpp:124:20: note: 'split_link' was declared here - 124 | LinkId split_link; - | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:20: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:812:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' @@ -6262,145 +6298,144 @@ make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/DependInfo.cmake "--color=" make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_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 -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu 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'/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/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/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends 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"--color=" +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build -make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/kmer_index/CMakeFiles/mph_index.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_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/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +[ 0%] Built target coverage_model make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/kmer_index/CMakeFiles/mph_index.dir/build'. +make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 2%] Built target mimalloc-obj +[ 4%] Built target version make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for '_deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build'. +make[5]: Nothing to be done for 'common/kmer_index/CMakeFiles/mph_index.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -[ 0%] Built target gqf -[ 0%] Built target coverage_model -[ 0%] Built target edlib -[ 2%] Built target version -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -[ 4%] Built target format -[ 7%] Built target teamcity_gtest -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" -[ 9%] Built target mph_index -[ 9%] Built target binary_io -[ 11%] Built target mimalloc-obj +[ 7%] Built target format make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -[ 30%] Built target zlibstatic +[ 26%] Built target zlibstatic +[ 28%] Built target teamcity_gtest +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" +make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/depend +[ 28%] Built target gqf make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/bwa.dir/DependInfo.cmake "--color=" +[ 28%] Built target edlib make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +[ 28%] Built target mph_index +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -[ 52%] Built target llvm-support +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 30%] Built target binary_io make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.dir/build -[ 52%] Built target sequence -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 38%] Built target utils +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build +[ 54%] Built target samtools +[ 64%] Built target llvm-support +make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. +make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. +make[5]: Nothing to be done for 'ext/bwa/CMakeFiles/bwa.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 66%] Built target samtools -[ 69%] Built target bwa -[ 71%] Built target utils -make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" +[ 64%] Built target sequence make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' @@ -6408,82 +6443,83 @@ make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build -[ 71%] Built target samio make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 66%] Built target samio make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +[ 69%] Built target assembly_graph make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" -[ 73%] Built target assembly_graph -make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build [ 78%] Built target input +[ 73%] Built target bwa make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/depend +make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library/CMakeFiles/library.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/library/CMakeFiles/library.dir/build.make common/library/CMakeFiles/library.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/library/CMakeFiles/library.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 80%] Built target alignment -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" -[ 80%] Built target library +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build +[ 78%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. +make[5]: Nothing to be done for 'common/alignment/CMakeFiles/alignment.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build -[ 83%] Built target modules -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/configs/CMakeFiles/configs.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" -[ 85%] Built target configs +[ 80%] Built target alignment +[ 83%] Built target configs make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build -make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. -make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" -[ 88%] Built target paired_info +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules 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'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 92%] Built target path_extend +[ 85%] Built target modules +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend +[ 90%] Built target path_extend +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. +make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' +[ 92%] Built target paired_info [ 92%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' @@ -6509,22 +6545,22 @@ make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -[ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -[ 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 -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/cyclic_hash_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/sequence_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/quality_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/nucl_test.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/sequence_test.cpp -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp +cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/cyclic_hash_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/test.cpp +[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/binary_test.cpp -cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/quality_test.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:462:26, @@ -6733,10 +6769,10 @@ make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_test -O--sourcedirectory=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-4.0.0+dfsg1/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-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu @@ -6899,38 +6935,38 @@ 1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down -1: [==========] 58 tests from 7 test suites ran. (1 ms total) +1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. -1/2 Test #1: include_test ..................... Passed 0.02 sec +1/2 Test #1: include_test ..................... Passed 0.01 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 100 tests from 11 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty -2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.015 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.Empty (19 ms) +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex -2: 0:00:00.020 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.021 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.OneVertex (1 ms) +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.021 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.021 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.022 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.000 1M / 9M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) -2: [----------] 6 tests from GraphCore (22 ms total) +2: [----------] 6 tests from GraphCore (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic @@ -6947,7 +6983,7 @@ 2: [ RUN ] PairedInfo.Remove 2: [ OK ] PairedInfo.Remove (0 ms) 2: [ RUN ] PairedInfo.UnexistingEdges -2: [ OK ] PairedInfo.UnexistingEdges (2 ms) +2: [ OK ] PairedInfo.UnexistingEdges (0 ms) 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours @@ -6963,10 +6999,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.025 1M / 8M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.027 1M / 8M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (89 ms) -2: [----------] 13 tests from PairedInfo (92 ms total) +2: 0:00:00.001 1M / 9M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.001 1M / 9M INFO GraphCore (graph_core.hpp : 690) 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 @@ -7009,917 +7045,917 @@ 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest -2: 0:00:00.115 1M / 10M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.120 1M / 10M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (16 ms) +2: 0:00:00.038 1M / 11M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.038 1M / 11M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.040 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (2 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.131 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.131 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.131 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.131 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.132 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.132 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance +2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.041 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.041 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.042 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.042 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.133 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.133 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.133 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.133 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.133 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.133 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance -2: [ OK ] Simplification.TipobulgeTest (1 ms) +2: 0:00:00.043 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.043 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.043 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.043 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.043 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.043 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance +2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.134 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.139 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.139 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.139 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.195 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (170 ms) +2: 0:00:00.044 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.044 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.044 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.044 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.067 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (69 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:00.305 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.306 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.306 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.306 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.374 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (183 ms) +2: 0:00:00.114 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.114 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.114 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.114 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.136 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (72 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:00.488 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.495 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.506 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.522 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.613 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (236 ms) +2: 0:00:00.186 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.187 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.187 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.187 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.209 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (65 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:00.729 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.742 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.758 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.766 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.838 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:00.842 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology -2: 0:00:00.871 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (240 ms) +2: 0:00:00.252 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.253 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.253 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.253 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.275 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.275 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology +2: 0:00:00.283 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (74 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:00.968 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.970 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:00.970 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp -2: 0:00:00.970 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:01.007 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:01.011 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (193 ms) +2: 0:00:00.327 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.327 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.327 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp +2: 0:00:00.327 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:00.343 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:00.343 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (76 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:01.162 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.166 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:01.166 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:01.166 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:01.168 1M / 51M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:01.173 1M / 51M INFO General (simplification_test.cpp : 277) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (11 ms) +2: 0:00:00.404 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.404 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.404 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.404 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.405 1M / 50M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.405 1M / 50M INFO General (simplification_test.cpp : 277) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (2 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:01.174 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.174 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:01.174 1M / 51M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:01.174 1M / 51M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:01.174 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.226 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:01.226 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) -2: 0:00:01.283 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:01.405 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:01.408 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:01.467 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.470 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (510 ms) +2: 0:00:00.406 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.406 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.406 1M / 50M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:00.406 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.406 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.426 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:00.426 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) +2: 0:00:00.454 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:00.511 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:00.511 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:00.540 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:00.540 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (215 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:01.684 1M / 53M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.686 1M / 53M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:01.686 1M / 53M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:01.686 1M / 53M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp -2: 0:00:01.687 1M / 53M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:01.947 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:01.951 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) -2: 0:00:01.999 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:02.098 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). -2: 0:00:02.099 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:02.176 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:02.176 1161M / 1161M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: [ OK ] Simplification.BigComplexBulge (647 ms) +2: 0:00:00.621 1M / 55M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.621 1M / 55M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.621 1M / 55M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:00.621 1M / 55M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp +2: 0:00:00.621 1M / 55M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.723 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:00.724 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) +2: 0:00:00.746 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:00.785 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). +2: 0:00:00.785 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:00.814 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:00.814 1161M / 1161M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: [ OK ] Simplification.BigComplexBulge (273 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:02.332 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.334 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:02.334 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:02.335 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp -2: 0:00:02.335 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:02.337 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:02.337 1M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) -2: 0:00:02.343 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:02.397 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). -2: 0:00:02.400 2M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:02.430 2M / 157M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:02.431 2M / 157M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:02.431 2M / 157M INFO General (simplification_test.cpp : 309) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (187 ms) +2: 0:00:00.895 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.895 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.895 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:00.895 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp +2: 0:00:00.895 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.897 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.898 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) +2: 0:00:00.902 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:00.928 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:00.928 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:00.940 2M / 159M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:00.940 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:00.940 2M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (87 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:02.519 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.523 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:02.523 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:02.523 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:02.523 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:02.564 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:02.566 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) -2: 0:00:02.622 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:02.737 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:02.738 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:02.797 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:02.800 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:02.800 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (464 ms) +2: 0:00:00.984 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.984 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:00.984 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:00.984 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:00.984 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.002 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:01.003 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) +2: 0:00:01.030 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.085 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:01.085 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.114 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.114 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:01.114 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (211 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:02.984 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.986 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:02.987 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:02.987 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp -2: 0:00:02.987 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:02.987 3M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:02.988 3M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) -2: 0:00:02.988 3M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:02.991 3M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). -2: 0:00:03.002 3M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:03.024 3M / 157M INFO General (graphio.cpp : 184) No positions were saved -2: 0:00:03.034 3M / 157M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:03.035 3M / 157M INFO General (simplification_test.cpp : 309) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (67 ms) +2: 0:00:01.194 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.194 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.194 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.194 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:01.194 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:01.195 3M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:01.195 3M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) +2: 0:00:01.195 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.197 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:01.197 3M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.198 3M / 159M INFO General (graphio.cpp : 184) No positions were saved +2: 0:00:01.198 3M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:01.198 3M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (12 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:03.052 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.055 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.055 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.055 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:03.055 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:03.055 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:03.055 1M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) -2: 0:00:03.056 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.056 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). -2: 0:00:03.057 1M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:03.057 1M / 157M INFO General (graphio.cpp : 184) No positions were saved -2: 0:00:03.057 1M / 157M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:03.057 1M / 157M INFO General (simplification_test.cpp : 309) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (9 ms) +2: 0:00:01.207 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.207 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.207 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.207 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:01.207 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:01.208 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:01.208 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) +2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:01.209 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.209 1M / 159M INFO General (graphio.cpp : 184) No positions were saved +2: 0:00:01.209 1M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:01.209 1M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (3 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:03.061 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.067 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.067 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.067 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp -2: 0:00:03.067 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:03.068 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:03.068 4M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) -2: 0:00:03.069 4M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.077 4M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). -2: 0:00:03.078 4M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:03.082 4M / 157M INFO General (graphio.cpp : 184) No positions were saved -2: 0:00:03.083 4M / 157M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:03.087 4M / 157M INFO General (simplification_test.cpp : 309) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (57 ms) +2: 0:00:01.211 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.211 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.211 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.211 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:01.211 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:01.211 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:01.211 4M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) +2: 0:00:01.212 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.217 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:01.217 4M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.218 4M / 159M INFO General (graphio.cpp : 184) No positions were saved +2: 0:00:01.219 4M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:01.219 4M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (21 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:03.119 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.123 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.123 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.123 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:03.123 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:03.123 2M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:03.123 2M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) -2: 0:00:03.124 2M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.124 2M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). -2: 0:00:03.124 2M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:03.125 2M / 157M INFO General (graphio.cpp : 184) No positions were saved -2: 0:00:03.125 2M / 157M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (11 ms) -2: [----------] 17 tests from Simplification (3015 ms total) +2: 0:00:01.232 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.232 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.232 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.232 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:01.232 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:01.233 2M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:01.233 2M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) +2: 0:00:01.233 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.233 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:01.233 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.233 2M / 159M INFO General (graphio.cpp : 184) No positions were saved +2: 0:00:01.233 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (2 ms) +2: [----------] 17 tests from Simplification (1195 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:03.130 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.130 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.131 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.131 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.131 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.131 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.131 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.149 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 2 reads -2: 0:00:03.149 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.159 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. -2: 0:00:03.160 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.160 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.160 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.160 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.160 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.180 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. -2: 0:00:03.181 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.185 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. -2: 0:00:03.185 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.189 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). -2: 0:00:03.191 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.194 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.194 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.195 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.196 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.198 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:03.198 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.198 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.198 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.198 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.198 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create -2: 0:00:03.198 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create -2: 0:00:03.199 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (69 ms) +2: 0:00:01.234 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.234 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.234 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.234 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.234 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.234 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.234 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.241 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 2 reads +2: 0:00:01.241 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.243 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. +2: 0:00:01.243 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.243 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.243 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.243 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.243 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.248 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. +2: 0:00:01.248 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.250 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. +2: 0:00:01.250 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.251 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:01.251 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.264 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.264 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.264 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.264 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.265 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:01.265 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.265 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.265 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.265 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create +2: 0:00:01.265 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (33 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:03.200 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.200 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.200 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.200 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.200 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.200 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.200 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.224 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 4 reads -2: 0:00:03.224 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.228 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. -2: 0:00:03.231 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.231 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.231 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.231 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.231 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.250 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. -2: 0:00:03.251 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.262 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. -2: 0:00:03.264 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.266 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). -2: 0:00:03.266 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.270 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.271 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.275 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.275 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.275 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:03.275 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.276 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.276 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.276 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create -2: 0:00:03.276 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (77 ms) +2: 0:00:01.267 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.267 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.267 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.267 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.268 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.268 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.268 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.275 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads +2: 0:00:01.276 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.277 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. +2: 0:00:01.277 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.277 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.277 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.277 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.277 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.283 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. +2: 0:00:01.284 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.285 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. +2: 0:00:01.285 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.286 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:01.286 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.360 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.360 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.360 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.360 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.360 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:01.360 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.360 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.360 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.360 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.360 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create +2: 0:00:01.360 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.360 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.360 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.360 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.361 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.361 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create +2: 0:00:01.361 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (94 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:03.277 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.277 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.277 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.277 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.277 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.277 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.277 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.300 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 4 reads -2: 0:00:03.301 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.308 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. -2: 0:00:03.308 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.308 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.308 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.308 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.308 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.336 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. -2: 0:00:03.337 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.341 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. -2: 0:00:03.341 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.342 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:03.343 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.344 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.345 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.345 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.345 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.345 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:03.345 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.345 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.345 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.345 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create -2: 0:00:03.346 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (71 ms) +2: 0:00:01.361 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.361 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.362 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.362 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.362 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.362 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.362 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.368 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads +2: 0:00:01.369 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.370 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. +2: 0:00:01.370 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.370 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.370 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.370 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.370 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.376 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. +2: 0:00:01.376 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.378 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. +2: 0:00:01.378 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.378 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:01.378 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.430 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.430 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.431 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.431 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.431 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:01.431 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.431 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.431 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.431 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create +2: 0:00:01.431 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (78 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:03.348 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.349 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.349 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.349 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.349 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.349 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.349 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.375 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 4 reads -2: 0:00:03.379 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.385 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. -2: 0:00:03.386 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.394 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.395 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.395 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.395 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.413 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. -2: 0:00:03.414 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.417 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. -2: 0:00:03.418 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.420 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). -2: 0:00:03.421 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.423 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.427 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.428 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.428 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.429 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:03.429 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.429 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.429 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.429 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create -2: 0:00:03.429 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (83 ms) +2: 0:00:01.440 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.440 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.440 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.440 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.440 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.440 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.440 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.447 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads +2: 0:00:01.447 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.449 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. +2: 0:00:01.449 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.449 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.449 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.449 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.449 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.453 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. +2: 0:00:01.454 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.455 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. +2: 0:00:01.455 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.456 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:01.456 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.535 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.536 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.536 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.536 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.536 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:01.536 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.536 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.536 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.536 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create +2: 0:00:01.536 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (99 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:03.431 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.434 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.436 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.436 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.436 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.436 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.436 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.455 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 4 reads -2: 0:00:03.467 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.470 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. -2: 0:00:03.474 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.479 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.483 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.494 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.495 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.519 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. -2: 0:00:03.520 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.525 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. -2: 0:00:03.525 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.528 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:03.534 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.539 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.540 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.540 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.540 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.540 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:03.540 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.540 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.541 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.541 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create -2: 0:00:03.541 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (110 ms) +2: 0:00:01.540 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.540 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.540 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.540 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.540 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.540 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.540 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.547 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads +2: 0:00:01.547 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.548 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. +2: 0:00:01.548 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.548 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.549 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.549 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.549 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.552 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. +2: 0:00:01.553 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.554 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. +2: 0:00:01.554 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.555 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:01.555 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.555 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.556 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.556 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.556 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.556 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:01.556 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.556 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.556 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.556 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create +2: 0:00:01.556 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (33 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:03.542 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.542 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.542 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.542 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.542 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.543 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.550 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.583 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 8 reads -2: 0:00:03.598 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.609 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.623 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.638 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.655 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.675 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.675 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.695 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. -2: 0:00:03.695 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.698 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.698 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.703 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:03.710 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.713 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.714 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.714 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.722 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.727 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:03.727 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.727 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.727 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.727 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create -2: 0:00:03.727 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (186 ms) +2: 0:00:01.574 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.574 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.574 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.574 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.574 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.574 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.574 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.592 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads +2: 0:00:01.592 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.594 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.594 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.594 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.594 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.594 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.594 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.600 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. +2: 0:00:01.601 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.602 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.602 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.603 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:01.603 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.604 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.604 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.604 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.604 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.604 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:01.604 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.604 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.604 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.604 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create +2: 0:00:01.604 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (52 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:03.728 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.734 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.738 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.739 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.739 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.739 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.739 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.739 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.771 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 8 reads -2: 0:00:03.771 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.774 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.775 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.775 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.775 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.775 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.775 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.796 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. -2: 0:00:03.796 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.802 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.802 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.803 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:03.810 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.815 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.816 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.816 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.816 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.817 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:03.817 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.817 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.817 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.817 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create -2: 0:00:03.817 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: 0:00:03.818 1M / 157M INFO General (graph_construction.hpp : 80) Building index with from graph -2: 0:00:03.818 1M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) -2: 0:00:03.818 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.818 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:03.818 1M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (97 ms) +2: 0:00:01.627 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.627 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.627 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.627 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.627 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.627 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.627 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.627 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.633 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads +2: 0:00:01.634 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.637 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.637 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.637 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.638 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.638 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.638 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.643 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. +2: 0:00:01.644 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.645 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.645 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.646 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:01.646 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.647 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.648 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.648 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.648 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.648 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:01.648 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.648 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.648 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.648 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create +2: 0:00:01.648 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: 0:00:01.648 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph +2: 0:00:01.648 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) +2: 0:00:01.648 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.648 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:01.648 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (22 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:03.826 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.827 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.827 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.831 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 -2: 0:00:03.838 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.840 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.840 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.840 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.872 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 8 reads -2: 0:00:03.872 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.875 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.881 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:03.886 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.894 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.902 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.902 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:03.931 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. -2: 0:00:03.943 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:03.950 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. -2: 0:00:03.955 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.960 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:03.960 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:03.961 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:03.961 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.961 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:03.961 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:03.961 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:03.962 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:03.962 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:03.962 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:03.962 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create -2: 0:00:03.962 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: 0:00:03.970 1M / 157M INFO General (graph_construction.hpp : 80) Building index with from graph -2: 0:00:03.970 1M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) -2: 0:00:03.971 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:03.971 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:03.971 1M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (145 ms) +2: 0:00:01.649 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.649 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.649 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.649 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 +2: 0:00:01.649 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.649 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.649 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.649 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.655 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads +2: 0:00:01.655 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.658 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.659 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.659 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.659 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.659 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.659 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.666 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. +2: 0:00:01.666 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.669 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. +2: 0:00:01.669 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.670 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:01.670 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.672 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.672 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.672 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.672 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.672 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:01.672 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.672 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.672 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.672 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create +2: 0:00:01.672 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: 0:00:01.672 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph +2: 0:00:01.673 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) +2: 0:00:01.673 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.673 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:01.673 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (24 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:03.972 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.972 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:03.972 1M / 157M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 -2: 0:00:03.972 1M / 157M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 -2: 0:00:03.972 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.972 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:03.972 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.972 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:04.008 1M / 157M INFO General (kmer_splitters.hpp : 134) Used 4 reads -2: 0:00:04.014 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:04.017 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. -2: 0:00:04.017 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index -2: 0:00:04.017 1M / 157M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.017 1M / 157M INFO General (file_limit.hpp : 43) Open file limit set to 1024 -2: 0:00:04.017 1M / 157M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.017 1M / 157M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 -2: 0:00:04.035 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. -2: 0:00:04.036 1M / 157M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. -2: 0:00:04.038 1M / 157M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. -2: 0:00:04.038 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:04.039 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). -2: 0:00:04.042 1M / 157M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. -2: 0:00:04.055 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers -2: 0:00:04.063 1M / 157M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.066 1M / 157M INFO General (graph_construction.hpp : 58) Condensing graph -2: 0:00:04.068 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths -2: 0:00:04.068 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:04.068 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops -2: 0:00:04.068 1M / 157M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.068 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... -2: 0:00:04.068 1M / 157M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted -2: 0:00:04.068 1M / 157M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create -2: 0:00:04.068 1M / 157M INFO General (debruijn_graph_constructor: 519) Collecting link records -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 521) Ordering link records -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 524) Sorting done -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create -2: 0:00:04.069 1M / 157M INFO General (debruijn_graph_constructor: 545) Connecting the graph -2: 0:00:04.069 1M / 157M INFO General (graph_construction.hpp : 80) Building index with from graph -2: 0:00:04.069 1M / 157M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) -2: 0:00:04.069 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:04.069 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). -2: 0:00:04.069 1M / 157M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. -2: 0:00:04.069 1M / 157M INFO General (graph_construction.hpp : 94) Filling coverage index -2: 0:00:04.069 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices -2: 0:00:04.070 1M / 157M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). -2: 0:00:04.070 1M / 157M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:04.070 1M / 157M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM -2: 0:00:04.072 1M / 157M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:04.082 1M / 157M INFO General (graph_pack_helpers.cpp : 56) Normalizing done -2: 0:00:04.101 14M / 157M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping -2: 0:00:04.113 14M / 157M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (162 ms) -2: [----------] 9 tests from GraphConstruction (1004 ms total) +2: 0:00:01.673 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.673 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.673 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 +2: 0:00:01.673 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 +2: 0:00:01.673 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.673 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.673 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.673 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.679 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads +2: 0:00:01.679 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.681 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. +2: 0:00:01.681 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index +2: 0:00:01.681 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:01.681 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 +2: 0:00:01.681 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:01.682 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 +2: 0:00:01.687 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. +2: 0:00:01.687 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. +2: 0:00:01.689 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. +2: 0:00:01.689 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.690 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). +2: 0:00:01.690 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. +2: 0:00:01.690 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers +2: 0:00:01.690 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. +2: 0:00:01.691 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph +2: 0:00:01.691 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths +2: 0:00:01.691 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:01.691 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops +2: 0:00:01.691 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected +2: 0:00:01.691 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... +2: 0:00:01.691 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create +2: 0:00:01.691 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph +2: 0:00:01.691 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph +2: 0:00:01.691 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) +2: 0:00:01.691 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.691 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). +2: 0:00:01.691 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. +2: 0:00:01.691 1M / 159M INFO General (graph_construction.hpp : 94) Filling coverage index +2: 0:00:01.691 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices +2: 0:00:01.692 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 446) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). +2: 0:00:01.692 1M / 159M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:01.692 1M / 159M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM +2: 0:00:01.692 1M / 159M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:01.692 1M / 159M INFO General (graph_pack_helpers.cpp : 56) Normalizing done +2: 0:00:01.696 14M / 159M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping +2: 0:00:01.697 14M / 159M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (27 ms) +2: [----------] 9 tests from GraphConstruction (466 ms total) 2: 2: [----------] 4 tests from Io 2: [ RUN ] Io.Order -2: 0:00:04.134 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.139 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.223 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.226 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (92 ms) +2: 0:00:01.700 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.700 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.736 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.736 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (35 ms) 2: [ RUN ] Io.PairedInfo -2: [ OK ] Io.PairedInfo (10 ms) +2: [ OK ] Io.PairedInfo (3 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [ RUN ] Io.GFADBG -2: 0:00:04.238 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.242 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.246 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:04.246 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:04.246 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:04.247 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.247 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.247 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.247 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.247 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp.grp -2: 0:00:04.247 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started -2: 0:00:04.250 49M / 157M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp -2: 0:00:04.262 49M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.262 49M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] Io.GFADBG (29 ms) -2: [----------] 4 tests from Io (133 ms total) +2: 0:00:01.740 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.740 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.740 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:01.740 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:01.740 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:01.740 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.740 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.741 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.741 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.741 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp.grp +2: 0:00:01.741 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started +2: 0:00:01.742 49M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp +2: 0:00:01.745 49M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.745 49M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: [ OK ] Io.GFADBG (7 ms) +2: [----------] 4 tests from Io (46 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:04.268 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.274 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.277 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.277 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.277 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathConstructor (9 ms) +2: 0:00:01.747 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.747 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.747 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.747 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathConstructor (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:04.277 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.277 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.277 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.277 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.278 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:04.278 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.278 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.278 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.278 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.279 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (4 ms) +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals -2: 0:00:04.282 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.283 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.283 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.283 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.283 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathEquals (1 ms) +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.748 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.748 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:04.283 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.283 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate -2: 0:00:04.284 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.284 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch -2: 0:00:04.284 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.284 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.284 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.285 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.285 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector -2: 0:00:04.285 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.285 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.285 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.285 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.285 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.749 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.749 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) -2: [----------] 8 tests from PathExtend (17 ms total) +2: [----------] 8 tests from PathExtend (2 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:04.286 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.286 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.286 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.286 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.286 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicNoDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:04.286 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.286 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.288 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.288 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.288 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicDiff (2 ms) +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:04.288 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.288 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.288 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:04.288 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:04.289 1M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:04.289 1M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.750 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:01.750 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:01.751 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:01.751 1M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:04.289 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.289 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.289 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.289 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.298 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.298 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (10 ms) +2: 0:00:01.751 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.751 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.751 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.751 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.756 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.756 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:04.299 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.299 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.299 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.299 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.307 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.310 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (12 ms) +2: 0:00:01.756 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.756 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.756 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.756 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.760 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.761 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:04.311 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.311 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.311 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.311 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.320 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.326 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.326 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (15 ms) +2: 0:00:01.761 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.761 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.761 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.761 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.765 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.765 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.765 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:04.327 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.327 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.327 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.327 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.335 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.338 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (12 ms) +2: 0:00:01.766 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.766 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.766 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.766 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.770 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.770 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:04.339 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.339 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.339 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.339 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.347 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.348 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.348 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (8 ms) +2: 0:00:01.770 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.770 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.770 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.770 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.775 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.775 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.775 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:04.348 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.348 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.348 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.348 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.357 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.357 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.357 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (9 ms) +2: 0:00:01.775 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.775 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.775 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.775 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.780 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.780 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.780 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:04.357 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.357 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.357 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.358 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.366 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.366 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.366 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (9 ms) +2: 0:00:01.780 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.780 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.780 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.780 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.784 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.784 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.784 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:04.367 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.367 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.367 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.367 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.375 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.378 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.378 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (12 ms) +2: 0:00:01.785 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.785 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.785 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.785 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.789 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.789 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.789 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:04.379 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.379 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.379 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.379 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.387 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (11 ms) +2: 0:00:01.790 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.790 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.790 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.790 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.794 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:04.391 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.391 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.391 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.391 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.399 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (9 ms) +2: 0:00:01.794 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.794 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.794 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.794 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.799 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:04.400 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.400 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.401 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.401 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.409 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (9 ms) +2: 0:00:01.799 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.799 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.799 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.799 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.804 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:04.410 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.410 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.410 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.410 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.418 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (10 ms) +2: 0:00:01.804 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.804 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.804 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.804 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.808 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:04.420 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.420 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.420 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.420 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.429 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (9 ms) +2: 0:00:01.809 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.809 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.809 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.809 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.813 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:04.429 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.429 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.430 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.430 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.438 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (9 ms) +2: 0:00:01.813 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.813 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.813 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.813 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.818 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (4 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:04.439 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.439 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.439 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.439 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.447 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.447 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.447 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (9 ms) +2: 0:00:01.818 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.818 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.818 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.818 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.823 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.823 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.823 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:04.448 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.448 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.448 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.448 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.456 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.456 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.456 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (9 ms) +2: 0:00:01.823 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.823 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.823 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.823 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.827 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.827 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.827 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:04.457 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.457 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.457 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.457 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.465 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.465 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.465 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (8 ms) +2: 0:00:01.828 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.828 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.828 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.828 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.832 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.832 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.832 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:04.466 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.466 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.466 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.466 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.474 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.474 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.474 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (9 ms) +2: 0:00:01.832 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.832 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.832 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.832 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.837 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.837 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.837 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (4 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:04.475 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.475 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.475 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.475 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.483 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.483 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.483 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (8 ms) +2: 0:00:01.837 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.837 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.837 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.837 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.842 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.842 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.842 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:04.483 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.484 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.484 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.484 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.492 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.492 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps -2: 0:00:04.492 4M / 157M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (9 ms) -2: [----------] 23 tests from OverlapRemoval (207 ms total) +2: 0:00:01.842 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.842 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.842 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.842 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.846 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.847 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps +2: 0:00:01.847 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (4 ms) +2: [----------] 23 tests from OverlapRemoval (97 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:04.493 1M / 157M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 +2: 0:00:01.847 1M / 159M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:04.493 1M / 157M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 -2: 0:00:04.493 1M / 157M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 +2: 0:00:01.847 1M / 159M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 +2: 0:00:01.847 1M / 159M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:04.493 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.493 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:04.493 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:04.493 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:04.501 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:04.502 4M / 157M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' -2: 0:00:04.510 5M / 157M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (808 ms) +2: 0:00:01.847 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.847 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:01.847 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:01.847 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:01.851 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:01.852 4M / 159M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' +2: 0:00:01.857 5M / 159M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (439 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:05.302 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.302 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:05.302 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.302 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.310 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (10 ms) +2: 0:00:02.286 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.286 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:02.286 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.286 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.291 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraOneEdgeTest (5 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest -2: 0:00:05.312 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.312 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:05.312 1M / 157M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.312 1M / 157M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.320 4M / 157M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraGrowEndsTest (9 ms) -2: [----------] 5 tests from GraphAligner (828 ms total) +2: 0:00:02.291 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.291 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:02.291 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:02.291 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:02.296 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraGrowEndsTest (5 ms) +2: [----------] 5 tests from GraphAligner (449 ms total) 2: 2: [----------] 1 test from VariableOverlaps 2: [ RUN ] VariableOverlaps.BasicOperations -2: 0:00:05.321 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.321 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: 0:00:05.322 1M / 157M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.322 1M / 157M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 -2: [ OK ] VariableOverlaps.BasicOperations (1 ms) -2: [----------] 1 test from VariableOverlaps (1 ms total) +2: 0:00:02.296 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.296 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: 0:00:02.297 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.297 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 +2: [ OK ] VariableOverlaps.BasicOperations (0 ms) +2: [----------] 1 test from VariableOverlaps (0 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 100 tests from 11 test suites ran. (5322 ms total) +2: [==========] 100 tests from 11 test suites ran. (2297 ms total) 2: [ PASSED ] 100 tests. -2/2 Test #2: debruijn_test .................... Passed 5.34 sec +2/2 Test #2: debruijn_test .................... Passed 2.30 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 5.36 sec +Total Test time (real) = 2.31 sec make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src -O--buildsystem=cmake dh_prep -O--sourcedirectory=src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/spades-4.0.0\+dfsg1/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-4.0.0\+dfsg1/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-4.0.0+dfsg1/src -B/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -7941,36 +7977,36 @@ -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/toy.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/config.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/sewage_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/pe_params.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/config.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/simplification.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/sewage_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/pe_params.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/sewage/usher_barcodes.csv -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades.py @@ -7983,55 +8019,55 @@ -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/coronaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executors.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_save_yaml.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_local.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/SeqIO.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/sam_parser.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/__init__.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/alignment.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/compress_all.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/copy_files.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/check_test_script.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/compress_all.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/correction_iteration_script.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/copy_files.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_parser.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_storage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_save_yaml.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executors.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/executors/executor_local.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/support.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/__init__.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/before_start_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/check_test_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/correction_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/scaffold_correction_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/preprocess_reads_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/error_correction_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/pipeline.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/terminating_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/scaffold_correction_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/pipeline.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/error_correction_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/preprocess_reads_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/check_test_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_stage.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/support.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/__init__.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/parallel_launcher.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/sam_parser.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/SeqIO.py --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/alignment.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/before_start_stage.py +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.gff --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.gff --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.txt +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.txt +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid --- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz +-- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gmapper @@ -8086,8 +8122,8 @@ dh_gencontrol -O--sourcedirectory=src -O--buildsystem=cmake dh_md5sums -O--sourcedirectory=src -O--buildsystem=cmake dh_builddeb -O--sourcedirectory=src -O--buildsystem=cmake -dpkg-deb: building package 'spades' in '../spades_4.0.0+dfsg1-1_amd64.deb'. dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_4.0.0+dfsg1-1_amd64.deb'. +dpkg-deb: building package 'spades' in '../spades_4.0.0+dfsg1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_4.0.0+dfsg1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_4.0.0+dfsg1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -8095,12 +8131,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3857398/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3857398/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/2534532 and its subdirectories -I: Current time: Fri Nov 15 11:18:45 -12 2024 -I: pbuilder-time-stamp: 1731712725 +I: removing directory /srv/workspace/pbuilder/3857398 and its subdirectories +I: Current time: Fri Dec 19 19:52:03 +14 2025 +I: pbuilder-time-stamp: 1766123523