I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 23 21:10:37 +14 2026 I: pbuilder-time-stamp: 1774249837 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [spades_4.0.0+dfsg1-2.dsc] I: copying [./spades_4.0.0+dfsg1.orig.tar.xz] I: copying [./spades_4.0.0+dfsg1-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./spades_4.0.0+dfsg1-2.dsc: unsupported subcommand dpkg-source: info: extracting spades in spades-4.0.0+dfsg1 dpkg-source: info: unpacking spades_4.0.0+dfsg1.orig.tar.xz dpkg-source: info: unpacking spades_4.0.0+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0101_cmake_ignore_removed_python-yaml.patch dpkg-source: info: applying 0102_cmake_ignore_removed_python-joblib.patch dpkg-source: info: applying bamtools-cmake.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch dpkg-source: info: applying debuginfo.patch dpkg-source: info: applying debian_bwa_zlib.patch dpkg-source: info: applying workdir_for_test.patch dpkg-source: info: applying disable_local_convertutf.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying use_debian_xxhash.patch dpkg-source: info: applying use_debian_cuckoo.patch dpkg-source: info: applying samtools_missing_source.patch dpkg-source: info: applying deactivate_tests_with_no_data.patch dpkg-source: info: applying raw_regex_pattern.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3074602/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 23 07:10 /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/3074602/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3074602/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=23efad364e844ea99ab8707f0dc71b51 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=3074602 PS4='+ ' 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.ojK6xN1t/pbuilderrc_17e1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ojK6xN1t/b2 --logfile b2/build.log spades_4.0.0+dfsg1-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3074602/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, asciidoctor, clang-format, clang-tidy, clang-tools, cmake, libbam-dev, libbamtools-dev, libbz2-dev, libboost-thread-dev, libc++-dev, libcuckoo-dev, libgtest-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libparallel-hashmap-dev, libspoa-dev, libssw-dev, libxxhash-dev, libzstd-dev, llvm-dev, lynx, python3-all, python3-joblib, python3-yaml, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19848 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on clang-format; however: Package clang-format is not installed. pbuilder-satisfydepends-dummy depends on clang-tidy; however: Package clang-tidy is not installed. pbuilder-satisfydepends-dummy depends on clang-tools; however: Package clang-tools is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libc++-dev; however: Package libc++-dev is not installed. pbuilder-satisfydepends-dummy depends on libcuckoo-dev; however: Package libcuckoo-dev is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-dev; however: Package libnlopt-dev is not installed. pbuilder-satisfydepends-dummy depends on libnlopt-cxx-dev; however: Package libnlopt-cxx-dev is not installed. pbuilder-satisfydepends-dummy depends on libparallel-hashmap-dev; however: Package libparallel-hashmap-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libxxhash-dev; however: Package libxxhash-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on llvm-dev; however: Package llvm-dev is not installed. pbuilder-satisfydepends-dummy depends on lynx; however: Package lynx is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} clang-19{a} clang-format{a} clang-format-19{a} clang-tidy{a} clang-tidy-19{a} clang-tools{a} clang-tools-19{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.2{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libc++-19-dev{a} libc++-dev{a} libc++1-19{a} libc++abi-19-dev{a} libc++abi1-19{a} libcereal-dev{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcuckoo-dev{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgc1{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} libllvm19{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libnsl2{a} libobjc-14-dev{a} libobjc4{a} libp11-kit-dev{a} libp11-kit0{a} libparallel-hashmap-dev{a} libpfm4{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libruby{a} libruby3.3{a} libsasl2-2{a} libsasl2-modules-db{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libtasn1-6{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libunwind-19{a} libunwind-19-dev{a} libuv1t64{a} libxml2{a} libxml2-dev{a} libxxhash-dev{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzstd-dev{a} llvm{a} llvm-19{a} llvm-19-dev{a} llvm-19-linker-tools{a} llvm-19-runtime{a} llvm-19-tools{a} llvm-dev{a} llvm-runtime{a} lynx{a} lynx-common{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-joblib{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-pygments{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} rake{a} rapidjson-dev{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.3{a} rubygems-integration{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support bzip2-doc fonts-lato krb5-locales libarchive-cpio-perl libclang-rt-19-dev libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults mailcap psmisc publicsuffix python3-numpy python3-psutil python3-pytest ruby-sdbm systemd zip 0 packages upgraded, 231 newly installed, 0 to remove and 0 not upgraded. Need to get 243 MB of archives. After unpacking 1369 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.9-1 [817 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.9-1 [2163 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.19 [5488 B] Get: 32 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 ruby-did-you-mean all 1.6.3-2 [20.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 ruby-minitest all 5.25.4-2 [66.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 ruby-power-assert all 2.0.3-1 [11.8 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 ruby-test-unit all 3.6.2-1 [79.1 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libruby3.3 amd64 3.3.7-1 [6274 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ruby3.3 amd64 3.3.7-1 [827 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.3+b1 [5440 B] Get: 44 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.6.3-1 [406 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.3+b1 [6560 B] Get: 46 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-1+b1 [26.0 MB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.7-1+b1 [13.2 MB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14.2.0-17 [42.7 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-17 [170 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.7-1+b1 [740 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.7-1+b1 [1261 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.7-1+b1 [7614 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.7-1+b1 [116 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 clang-format-19 amd64 1:19.1.7-1+b1 [92.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 clang-format amd64 1:19.0-63 [6352 B] Get: 68 http://deb.debian.org/debian unstable/main amd64 clang-tools-19 amd64 1:19.1.7-1+b1 [8961 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 clang-tidy-19 amd64 1:19.1.7-1+b1 [1883 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 clang-tidy amd64 1:19.0-63 [6116 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 clang-tools amd64 1:19.0-63 [6164 B] Get: 73 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.5-2 [2267 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 80 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.5-2 [12.0 MB] Get: 100 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 107 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 119 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 googletest all 1.16.0-1 [517 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.1 [10.6 MB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1 [234 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1 [235 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.1 [240 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.1 [246 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.1 [230 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1 [333 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1 [373 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.1 [239 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1 [230 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1 [232 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1 [269 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.1 [276 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libunwind-19 amd64 1:19.1.7-1+b1 [63.0 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libc++abi1-19 amd64 1:19.1.7-1+b1 [105 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libc++1-19 amd64 1:19.1.7-1+b1 [303 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libc++abi-19-dev amd64 1:19.1.7-1+b1 [128 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libunwind-19-dev amd64 1:19.1.7-1+b1 [81.5 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libc++-19-dev amd64 1:19.1.7-1+b1 [1285 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libc++-dev amd64 1:19.0-63 [6056 B] Get: 159 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libcuckoo-dev all 0.3.1-3 [37.5 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-2 [479 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.7-1 [60.8 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libgtest-dev amd64 1.16.0-1 [259 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250125-2 [105 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250125-2 [353 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b2 [178 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-6+b2 [46.9 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-6+b2 [205 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-6+b2 [13.5 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libparallel-hashmap-dev all 1.4.1+ds-1 [205 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.9-1 [1974 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libspoa7.0.0 amd64 4.1.4-2+b1 [74.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libspoa-dev amd64 4.1.4-2+b1 [9808 B] Get: 214 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b2 [24.6 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libxxhash-dev amd64 0.8.3-2 [81.0 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.7-1+b1 [551 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 llvm-runtime amd64 1:19.0-63 [5904 B] Get: 221 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.7-1+b1 [16.4 MB] Get: 222 http://deb.debian.org/debian unstable/main amd64 llvm amd64 1:19.0-63 [8328 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.7-1+b1 [511 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.7-1+b1 [43.2 MB] Get: 226 http://deb.debian.org/debian unstable/main amd64 llvm-dev amd64 1:19.0-63 [6152 B] Get: 227 http://deb.debian.org/debian unstable/main amd64 lynx-common all 2.9.2-1 [1193 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.9-1 [681 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.1-2 [1056 B] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-2 [216 kB] Fetched 243 MB in 4s (59.2 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19848 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../194-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package libparallel-hashmap-dev. Preparing to unpack .../195-libparallel-hashmap-dev_1.4.1+ds-1_all.deb ... Unpacking libparallel-hashmap-dev (1.4.1+ds-1) ... Selecting previously unselected package libpfm4:amd64. Preparing to unpack .../196-libpfm4_4.13.0+git83-g91970fe-1_amd64.deb ... Unpacking libpfm4:amd64 (4.13.0+git83-g91970fe-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../197-libpython3.12-stdlib_3.12.9-1_amd64.deb ... 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Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20250104-1) ... Setting up libboost-system1.83.0:amd64 (1.83.0-4.1) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpython3.12-minimal:amd64 (3.12.9-1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.23-1+b1) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-4.1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libnlopt0:amd64 (2.7.1-6+b2) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libc++abi1-19:amd64 (1:19.1.7-1+b1) ... Setting up googletest (1.16.0-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up rapidjson-dev (1.1.0+dfsg2-7.3) ... 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Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libspoa-dev:amd64 (4.1.4-2+b1) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.1-2) ... Setting up rubygems-integration (1.19) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up clang-19 (1:19.1.7-1+b1) ... Setting up clang-tools-19 (1:19.1.7-1+b1) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up llvm-runtime:amd64 (1:19.0-63) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up lynx (2.9.2-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up clang-tools:amd64 (1:19.0-63) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.9-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libcurl4t64:amd64 (8.12.1-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up python3-joblib (1.4.2-2) ... Setting up clang-format-19 (1:19.1.7-1+b1) ... Setting up python3.12 (3.12.9-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-2) ... 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Setting up libcurl4-gnutls-dev:amd64 (8.12.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up rake (13.2.1-1) ... Setting up libruby3.3:amd64 (3.3.7-1) ... Setting up ruby-rubygems (3.6.3-1) ... Setting up ruby3.3 (3.3.7-1) ... Setting up libruby:amd64 (1:3.3+b1) ... Setting up ruby (1:3.3+b1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3074602/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3074602/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+dfsg1-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 4.0.0+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_clean find . -name "*.pyc" -delete rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.html /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? rm -rf /build/reproducible-path/spades-4.0.0+dfsg1/debian/man make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_autoreconf_clean -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_clean -X.orig make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' debian/rules binary dh binary --sourcedirectory=src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH="/usr" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBoost_NO_BOOST_CMAKE=TRUE -DSPADES_BOOST_ROOT:PATH=/usr ../src -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found bamtools: /usr/lib/x86_64-linux-gnu/libbamtools.so -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libncurses.so - found -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so -- Looking for wsyncup in /usr/lib/x86_64-linux-gnu/libcurses.so - found CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0144 is not set: find_package uses upper-case _ROOT variables. Run "cmake --help-policy CMP0144" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMake variable BOOST_ROOT is set to: SPADES_BOOST_ROOT For compatibility, find_package is ignoring the variable, but code in a .cmake module might still use it. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/deps.cmake:29 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:66 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/include (found version "1.83.0") Making Release Configuration... -- Building SPAdes version 4.0.0 Building SPAdes from N/A, sha: N/A CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- -- Override standard malloc (MI_OVERRIDE=ON) -- Enable abort() calls on memory allocation failure (MI_XMALLOC=ON) -- Enable printing of error and warning messages by default (MI_SHOW_ERRORS=ON) -- Use the C++ compiler to compile (MI_USE_CXX=ON) -- -- Library base name: mimalloc -- Version : 2.0 -- Build type : none -- C++ Compiler : /usr/bin/c++ -- Compiler flags : -Wall;-Wextra;-Wno-unknown-pragmas;-fvisibility=hidden;-ftls-model=initial-exec;-fno-builtin-malloc -- Compiler defines : MI_XMALLOC=1;MI_SHOW_ERRORS=1 -- Link libraries : /usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a -- Build targets : object -- CMake Warning (dev) at /usr/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message): Calling FetchContent_Populate(zlib_ng) is deprecated, call FetchContent_MakeAvailable(zlib_ng) instead. Policy CMP0169 can be set to OLD to allow FetchContent_Populate(zlib_ng) to be called directly for now, but the ability to call it with declared details will be removed completely in a future version. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/CMakeLists.txt:20 (FetchContent_Populate) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Using CMake version 3.31.5 -- ZLIB_HEADER_VERSION: 1.3.0 -- ZLIBNG_HEADER_VERSION: 2.1.4 -- Arch detected: 'x86_64' -- Basearch of 'x86_64' has been detected as: 'x86' -- Performing Test FNO_LTO_AVAILABLE -- Performing Test FNO_LTO_AVAILABLE - Success -- Looking for arm_acle.h -- Looking for arm_acle.h - not found -- Looking for sys/auxv.h -- Looking for sys/auxv.h - found -- Looking for sys/sdt.h -- Looking for sys/sdt.h - not found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for strerror -- Looking for strerror - found -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for aligned_alloc -- Looking for aligned_alloc - found -- Performing Test HAVE_NO_INTERPOSITION -- Performing Test HAVE_NO_INTERPOSITION - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_HIDDEN - Success -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL -- Performing Test HAVE_ATTRIBUTE_VISIBILITY_INTERNAL - Success -- Performing Test HAVE_ATTRIBUTE_ALIGNED -- Performing Test HAVE_ATTRIBUTE_ALIGNED - Success -- Performing Test HAVE_THREAD_LOCAL -- Performing Test HAVE_THREAD_LOCAL - Success -- Performing Test HAVE_BUILTIN_CTZ -- Performing Test HAVE_BUILTIN_CTZ - Success -- Performing Test HAVE_BUILTIN_CTZLL -- Performing Test HAVE_BUILTIN_CTZLL - Success -- Performing Test HAVE_PTRDIFF_T -- Performing Test HAVE_PTRDIFF_T - Success -- Performing Test HAVE_AVX2_INTRIN -- Performing Test HAVE_AVX2_INTRIN - Success -- Performing Test HAVE_CASCADE_LAKE -- Performing Test HAVE_CASCADE_LAKE - Success -- Performing Test HAVE_AVX512_INTRIN -- Performing Test HAVE_AVX512_INTRIN - Success -- Performing Test HAVE_MASK_INTRIN -- Performing Test HAVE_MASK_INTRIN - Success -- Performing Test HAVE_AVX512VNNI_INTRIN -- Performing Test HAVE_AVX512VNNI_INTRIN - Success -- Performing Test HAVE_SSE42_INTRIN -- Performing Test HAVE_SSE42_INTRIN - Success -- Performing Test HAVE_SSE2_INTRIN -- Performing Test HAVE_SSE2_INTRIN - Success -- Performing Test HAVE_SSSE3_INTRIN -- Performing Test HAVE_SSSE3_INTRIN - Success -- Performing Test HAVE_PCLMULQDQ_INTRIN -- Performing Test HAVE_PCLMULQDQ_INTRIN - Success -- Performing Test HAVE_VPCLMULQDQ_INTRIN -- Performing Test HAVE_VPCLMULQDQ_INTRIN - Success -- Performing Test HAVE_XSAVE_INTRIN -- Performing Test HAVE_XSAVE_INTRIN - Success -- Architecture-specific source files: arch/x86/x86_features.c;arch/x86/slide_hash_avx2.c;arch/x86/chunkset_avx2.c;arch/x86/compare256_avx2.c;arch/x86/adler32_avx2.c;arch/x86/adler32_avx512.c;arch/x86/adler32_avx512_vnni.c;arch/x86/adler32_sse42.c;arch/x86/insert_string_sse42.c;arch/x86/chunkset_sse2.c;arch/x86/compare256_sse2.c;arch/x86/slide_hash_sse2.c;arch/x86/adler32_ssse3.c;arch/x86/chunkset_ssse3.c;arch/x86/crc32_pclmulqdq.c;arch/x86/crc32_vpclmulqdq.c CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/test/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The following features have been enabled: * CMAKE_BUILD_TYPE, Build type: None (selected) * AVX2_SLIDEHASH, Support AVX2 optimized slide_hash, using "-mavx2" * AVX2_CHUNKSET, Support AVX2 optimized chunkset, using "-mavx2" * AVX2_COMPARE256, Support AVX2 optimized compare256, using "-mavx2" * AVX2_ADLER32, Support AVX2-accelerated adler32, using "-mavx2" * AVX512_ADLER32, Support AVX512-accelerated adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * AVX512VNNI_ADLER32, Support AVX512VNNI adler32, using "-mavx512f -mavx512dq -mavx512bw -mavx512vl -mavx512vnni -mtune=cascadelake" * SSE42_CRC, Support SSE4.2 optimized CRC hash generation, using "-msse4.2" * SSSE3_ADLER32, Support SSSE3-accelerated adler32, using "-mssse3" * PCLMUL_CRC, Support CRC hash generation using PCLMULQDQ, using "-mssse3 -msse4.2 -mpclmul" * VPCLMUL_CRC, Support CRC hash generation using VPCLMULQDQ, using "-mvpclmulqdq -mavx512f -mavx512f -mavx512dq -mavx512bw -mavx512vl -mtune=cascadelake" * XSAVE, Support XSAVE intrinsics using "-mxsave" * WITH_GZFILEOP, Compile with support for gzFile related functions * ZLIB_COMPAT, Compile with zlib compatible API * ZLIB_ENABLE_TESTS, Build test binaries * ZLIBNG_ENABLE_TESTS, Test zlib-ng specific API * WITH_SANITIZER, Enable sanitizer support * WITH_OPTIM, Build with optimisation * WITH_NEW_STRATEGIES, Use new strategies * WITH_AVX2, Build with AVX2 * WITH_AVX512, Build with AVX512 * WITH_AVX512VNNI, Build with AVX512 VNNI * WITH_SSE2, Build with SSE2 * WITH_SSSE3, Build with SSSE3 * WITH_SSE42, Build with SSE42 * WITH_PCLMULQDQ, Build with PCLMULQDQ * WITH_VPCLMULQDQ, Build with VPCLMULQDQ -- The following OPTIONAL packages have been found: * bamtools * OpenMP * Curses -- The following REQUIRED packages have been found: * BZip2 * Boost -- The following features have been disabled: * ZLIB_SYMBOL_PREFIX, Publicly exported symbols DO NOT have a custom prefix * WITH_GTEST, Build gtest_zlib * WITH_FUZZERS, Build test/fuzz * WITH_BENCHMARKS, Build test/benchmarks * WITH_BENCHMARK_APPS, Build application benchmarks * WITH_NATIVE_INSTRUCTIONS, Instruct the compiler to use the full instruction set on this host (gcc/clang -march=native) * WITH_MAINTAINER_WARNINGS, Build with project maintainer warnings * WITH_CODE_COVERAGE, Enable code coverage reporting * WITH_INFLATE_STRICT, Build with strict inflate distance checking * WITH_INFLATE_ALLOW_INVALID_DIST, Build with zero fill for inflate invalid distances * INSTALL_UTILS, Copy minigzip and minideflate during install -- The following OPTIONAL packages have not been found: * Readline -- Looking for open -- Looking for open - found -- Looking for execinfo.h -- Looking for execinfo.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for cxxabi.h -- Looking for cxxabi.h - not found -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- Looking for mach/mach.h -- Looking for mach/mach.h - not found -- Looking for link.h -- Looking for link.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for malloc/malloc.h -- Looking for malloc/malloc.h - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Looking for futimens -- Looking for futimens - found -- Looking for futimes -- Looking for futimes - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for mallinfo -- Looking for mallinfo - found -- Looking for mallctl -- Looking for mallctl - not found -- Looking for malloc_zone_statistics -- Looking for malloc_zone_statistics - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Looking for pthread_getspecific in pthread -- Looking for pthread_getspecific in pthread - found -- Looking for pthread_rwlock_init in pthread -- Looking for pthread_rwlock_init in pthread - found -- Looking for pthread_mutex_lock in pthread -- Looking for pthread_mutex_lock in pthread - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Performing Test HAVE_FFI_CALL -- Performing Test HAVE_FFI_CALL - Success -- Found FFI: /usr/lib/x86_64-linux-gnu/libffi.so -- Could NOT find LibEdit (missing: LibEdit_INCLUDE_DIRS LibEdit_LIBRARIES) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found zstd: /usr/lib/x86_64-linux-gnu/libzstd.so -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.12.1") -- Looking for shm_open -- Looking for shm_open - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/CMakeLists.txt:4 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Looking for include file endian.h -- Looking for include file endian.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/param.h -- Looking for include file sys/param.h - found -- Looking for include file sys/sysctl.h -- Looking for include file sys/sysctl.h - not found -- Looking for include file netinet/in.h -- Looking for include file netinet/in.h - found -- Performing Test eslENABLE_SSE -- Performing Test eslENABLE_SSE - Success -- Performing Test eslENABLE_SSE4 -- Performing Test eslENABLE_SSE4 - Failed -- Performing Test eslENABLE_AVX -- Performing Test eslENABLE_AVX - Failed -- Performing Test eslENABLE_AVX512 -- Performing Test eslENABLE_AVX512 - Failed -- Performing Test eslENABLE_NEON -- Performing Test eslENABLE_NEON - Failed -- Performing Test eslHAVE_NEON_AARCH64 -- Performing Test eslHAVE_NEON_AARCH64 - Failed -- Performing Test HAVE_FLUSH_ZERO_MODE -- Performing Test HAVE_FLUSH_ZERO_MODE - Success -- Performing Test HAVE_DENORMALS_ZERO_MODE -- Performing Test HAVE_DENORMALS_ZERO_MODE - Failed -- Looking for erfc -- Looking for erfc - not found -- Looking for getpid -- Looking for getpid - found -- Looking for _mm_malloc -- Looking for _mm_malloc - not found -- Looking for popen -- Looking for popen - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strsep -- Looking for strsep - found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for times -- Looking for times - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for stat -- Looking for stat - found CMake Deprecation Warning at /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/blaze/cmake/Blaze_Import.cmake:51 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. Call Stack (most recent call first): /build/reproducible-path/spades-4.0.0+dfsg1/ext/include/CMakeLists.txt:7 (Blaze_Import) -- Configuring blaze version 3.8 -- Configured C++11 for multithreading. -- Configuring Vectorization : ON -- Automatic Cache Size Configuration -- Configuring Cache Size : 16777216UL -- Blaze has been configured successfully -- Enabling BayesHammer as a dependency to SPAdes -- Enabling IonHammer as a dependency to SPAdes -- Enabling Corrector as a dependency to SPAdes -- spades project is enabled -- hammer project is enabled -- ionhammer project is enabled -- corrector project is enabled -- spaligner project is disabled -- spades_tools project is enabled -- binspreader project is disabled -- pathracer project is disabled -- mts project is disabled -- online_vis project is disabled -- cds_subgraphs project is disabled -- Configuring done (34.5s) -- Generating done (0.4s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /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' 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 -j12 "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 make -f CMakeFiles/Makefile2 all make[3]: 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/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[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/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/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' 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/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 -f 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'/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[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=" 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/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[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/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/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[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[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 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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[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 ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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[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/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build 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 common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.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]: 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[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[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]: 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 [ 0%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.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/ext/gqf && /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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 3%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o [ 3%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o [ 3%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.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 -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/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/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 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 -fno-builtin-malloc -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/src/static.c [ 3%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.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/adler32.c.o -MF CMakeFiles/zlibstatic.dir/adler32.c.o.d -o CMakeFiles/zlibstatic.dir/adler32.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/adler32.c [ 6%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o [ 6%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o [ 6%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o [ 6%] Building CXX object ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o [ 6%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 6%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.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/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 cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib && /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 -MD -MT ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/edlib/edlib.cpp 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 /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/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_gtest.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/lexy/src && /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/lexy/src/../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++20 -Wno-deprecated -O2 -pedantic-errors -Werror -Wall -Wextra -Wconversion -Wsign-conversion -Wno-parentheses -Wno-unused-local-typedefs -Wno-array-bounds -Wno-maybe-uninitialized -Wno-restrict -MD -MT ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o -MF CMakeFiles/lexy_file.dir/input/file.cpp.o.d -o CMakeFiles/lexy_file.dir/input/file.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/src/input/file.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/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 cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/coverage_model && /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/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -MF CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/coverage_model/kmer_coverage_model.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/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/easel.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); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_dump': /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 644 | qf->metadata->nblocks, 645 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c:643:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 643 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 646 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/gqf/gqf.c: In function 'qf_deserialize': /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%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_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/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 [ 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 [ 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 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/ext/lexy/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lexy_file.dir/link.txt --verbose=1 [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/chunkset.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/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 /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' /usr/bin/ar qc liblexy_file.a CMakeFiles/lexy_file.dir/input/file.cpp.o /usr/bin/ranlib liblexy_file.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 6%] Built target version [ 6%] 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 [ 6%] Built target lexy_file [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.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/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 [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.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/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 [ 6%] 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 [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.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/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 [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.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/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/CrashRecoveryContext.cpp [ 6%] 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 /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' [ 6%] Built target gqf [ 6%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o [ 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/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 /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/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/teamcity_gtest/teamcity_messages.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/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 [ 6%] 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 [ 6%] 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 [ 6%] 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 [ 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/_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/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 [ 7%] 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 [ 8%] 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 [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/crc32_braid.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_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 /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' [ 8%] Built target edlib [ 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 -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_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 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_buffer.c 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/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 -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' [ 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_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_cluster.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_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%] 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 make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+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=" /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); | ^~~~~~ make[4]: 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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 9%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/sequence && /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/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 [ 9%] 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 /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' [ 9%] Built target teamcity_gtest [ 9%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o 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/posix.cc.o -MF CMakeFiles/format.dir/posix.cc.o.d -o CMakeFiles/format.dir/posix.cc.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/cppformat/posix.cc [ 9%] 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 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]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:208:19: required from here 208 | graph_io_.Load(basename, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:211:45: required from here 211 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:214:34: required from here 214 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:217:35: required from here 217 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:220:41: required from here 220 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:102:14: warning: unused variable 'loaded' [-Wunused-variable] 102 | bool loaded = io.Load(basename, component); | ^~~~~~ /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/graph_pack.cpp:254:22: required from here 254 | graph_io_.BinRead(is, gp.get_mutable()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:257:45: required from here 257 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /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); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:260:34: required from here 260 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /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); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:263:35: required from here 263 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /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); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph_pack.cpp:266:41: required from here 266 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /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); | ^~~~~~ [ 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 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 [ 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/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) { | ^~~~~~~ /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_ ? | ^~~~~~~ [ 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_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 /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' [ 10%] Built target mph_index [ 10%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.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/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 [ 10%] 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 [ 12%] 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 [ 12%] 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 [ 12%] 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 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], | ^~~~~~ [ 12%] 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 [ 12%] 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 [ 12%] 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/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 [ 13%] Linking CXX static library libformat.a [ 13%] 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/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake 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/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Error.cpp 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 [ 14%] 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 /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' [ 14%] Built target format [ 14%] 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 [ 14%] 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 -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_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_dsqdata.c [ 14%] 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 [ 14%] 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 [ 14%] 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 [ 14%] 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 /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' [ 14%] Built target sequence [ 14%] 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/_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 [ 14%] 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 [ 14%] 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 [ 14%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 14%] 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=" [ 14%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o [ 14%] 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/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 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 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' [ 14%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+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/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/memory_limit.cpp [ 14%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.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/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 [ 14%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/insert_string_roll.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_roll.c.o -MF CMakeFiles/zlibstatic.dir/insert_string_roll.c.o.d -o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/insert_string_roll.c [ 14%] 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 [ 15%] 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 [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/slide_hash.c.o [ 17%] 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/_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/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 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 [ 17%] 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 [ 17%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/trees.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/trees.c.o -MF CMakeFiles/zlibstatic.dir/trees.c.o.d -o CMakeFiles/zlibstatic.dir/trees.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/trees.c [ 18%] 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/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 [ 18%] Building C object _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 -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/uncompr.c.o -MF CMakeFiles/zlibstatic.dir/uncompr.c.o.d -o CMakeFiles/zlibstatic.dir/uncompr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/uncompr.c [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.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_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 [ 18%] 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 [ 18%] 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 [ 18%] 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/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 [ 19%] 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 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/JSON.cpp [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o cd 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LEB128.cpp /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' [ 19%] Built target coverage_model [ 19%] 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 [ 19%] 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 [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/zutil.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/zutil.c.o -MF CMakeFiles/zlibstatic.dir/zutil.c.o.d -o CMakeFiles/zlibstatic.dir/zutil.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/zutil.c [ 19%] 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 [ 19%] 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 [ 19%] 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 [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_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/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 /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/slide_hash_avx2.c [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_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/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 [ 20%] 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 [ 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/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 [ 20%] 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 [ 21%] 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 [ 21%] 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 [ 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/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 [ 21%] 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 [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.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/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemAlloc.cpp [ 23%] 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 [ 23%] 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 [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.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/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MemoryBuffer.cpp [ 23%] 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 [ 23%] 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 [ 23%] 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 -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/NativeFormatting.cpp [ 23%] 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 [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_iset.c.o [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.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 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/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 [ 24%] 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 [ 24%] 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 [ 24%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 [ 24%] 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 [ 24%] 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 -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/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Program.cpp [ 25%] 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 /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 [ 25%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.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/_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 [ 25%] Built target utils [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 25%] 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 [ 26%] 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 [ 26%] 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 [ 26%] 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 [ 26%] 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 -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msacluster.c [ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o 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; | ^~~~~~~~ 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 [ 26%] 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 [ 28%] 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 C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o [ 29%] 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_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 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 [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.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_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_afa.c [ 29%] 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 [ 30%] 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 [ 30%] 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 [ 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 _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 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 [ 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 _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 [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o [ 30%] 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/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_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_clustal.c 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 [ 30%] 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 [ 30%] 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 [ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.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_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 [ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.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/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 [ 31%] 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 [ 32%] 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 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 [ 32%] 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 [ 32%] 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 /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 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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' [ 32%] Built target zlibstatic [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o [ 32%] 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 -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 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_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 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=" make[4]: 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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 34%] 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 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=" make[4]: 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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 34%] 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 [ 34%] 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 [ 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.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 make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+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[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' [ 35%] 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 [ 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 [ 36%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.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 [ 36%] 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 [ 36%] 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 [ 37%] 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_quicksort.c.o -MF CMakeFiles/easel.dir/esl_quicksort.c.o.d -o CMakeFiles/easel.dir/esl_quicksort.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_quicksort.c [ 37%] 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 [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o [ 37%] 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/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/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 [ 37%] 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 [ 37%] 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 -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 [ 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] 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 [ 39%] 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 [ 39%] 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 /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<>; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /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 + | ~~~~~~~~~~~~~~~ 72 | integer + | ~~~~~~~~~ 73 | dsl::if_(fraction) + | ~~~~~~~~~~~~~~~~~~~~ 74 | dsl::if_(exponent) + | ~~~~~~~~~~~~~~~~~~~^ 75 | dsl::position; | ~~~~~~~~~~~~~ /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:94:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 94 | dsl::capture(LEXY_LIT("A")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:95:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 95 | dsl::capture(LEXY_LIT("i")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:96:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 96 | dsl::capture(LEXY_LIT("f")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:97:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 97 | dsl::capture(LEXY_LIT("Z")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:98:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 98 | dsl::capture(LEXY_LIT("J")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:99:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 99 | dsl::capture(LEXY_LIT("H")) >> colon + dsl::p | | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:100:50: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 100 | dsl::capture(LEXY_LIT("B")) >> colon + dsl::p | ~~~~~~^~~~~~~~~~~~~~~~~~~~ [ 39%] 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 /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:162:40: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 162 | return dsl::eof | (tab >> tags + dsl::eof); | ~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp: At global scope: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:191:56: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 189 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 | tab + (LEXY_LIT("*") | | ~~~~~~~~~~~~~~~~~~~~~~ 191 | dsl::identifier(dsl::ascii::alpha)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 192 | dsl::p; | ~~~~~~~~~~~~~~~~ /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 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 213 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 215 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 216 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 217 | dsl::p; | ~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:246:54: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 244 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 | tab + dsl::p + | ~~~~~~~~~~~~~~~~~~~~~~~~ 246 | tab + (LEXY_LIT("*") | dsl::p) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 247 | dsl::p; | ~~~~~~~~~~~~~~~~ /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:269:41: warning: suggest parentheses around '+' inside '>>' [-Wparentheses] 269 | dsl::ascii::alpha >> tab + dsl::until(dsl::newline).or_eof() | | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 39%] 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 [ 39%] 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 [ 40%] 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 [ 40%] 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 /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)...)); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/detect.hpp:28:60: required from 'constexpr const bool lexy::_detail::is_detected using lexy::_detect_callback_for = decltype (declval()((declval)()...)), lexy::_callback >, unsigned int&, lexy::lexeme&&>' 28 | constexpr bool is_detected = _detector::value; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/callback/base.hpp:22:16: required from 'constexpr const bool lexy::is_callback_for >, unsigned int&, lexy::lexeme&&>' 22 | = _detail::is_detected<_detect_callback_for, std::decay_t, Args...>; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/grammar.hpp:353:34: required from 'constexpr lexy::production_value_callback::return_type lexy::production_value_callback::operator()(Args&& ...) const [with Args = {unsigned int&, lexy::lexeme}; Production = gfa::grammar::cigar_string::cigarop; ParseState = void; return_type = gfa::cigarop]' 353 | else if constexpr (lexy::is_callback_for<_type, Args&&...>) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/_detail/lazy_init.hpp:130:36: [ skipping 30 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:108:60: required from 'lexyd::_chc, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err >::p::parse, void, gfa::grammar::record, void>, lexy::_prd>(lexy::_pc, void, gfa::grammar::record, void>&, lexy::_prd&):: [with auto:42 = lexyd::_prd::bp]' 108 | result = parser.template finish(context, reader, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 109 | static_cast(args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/dsl/choice.hpp:114:39: required from 'static constexpr bool lexyd::_chc::p::parse(Context&, Reader&, Args&& ...) [with Context = lexy::_pc, void, gfa::grammar::record, void>; Reader = lexy::_prd; Args = {}; NextParser = lexy::_detail::final_parser; R = {lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_prd, lexyd::_br, lexyd::_until_eof >, lexyd::_br, lexyd::_until_eof >, lexyd::_err}]' 114 | auto found_branch = (try_r(lexy::branch_parser_for{}) || ...); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:210:37: required from 'constexpr auto lexy::_do_action(_pc&, Reader&) [with Handler = _ph<_prd>; State = void; Production = gfa::grammar::record; Reader = _prd; typename std::conditional<_production_defines_whitespace, Production, void>::type = void]' 210 | auto rule_result = parser::parse(context, reader); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/base.hpp:236:34: required from 'constexpr auto lexy::do_action(Handler&&, State*, Reader&) [with Production = gfa::grammar::record; Result = parse_action, lexy_ext::_report_error >::result_type; Handler = _ph<_prd>; State = void; Reader = _prd]' 236 | auto rule_result = _do_action(context, reader); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:164:56: required from 'constexpr auto lexy::parse_action::operator()(Production, const Input&) const [with Production = gfa::grammar::record; State = void; Input = lexy::string_input; ErrorCallback = lexy_ext::_report_error]' 164 | return lexy::do_action(handler(input_holder, sink), _state, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 | reader); | ~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/lexy/include/lexy/action/parse.hpp:173:62: required from 'constexpr auto lexy::parse(const Input&, const ErrorCallback&) [with Production = gfa::grammar::record; Input = string_input; ErrorCallback = lexy_ext::_report_error]' 173 | return parse_action(callback)(Production{}, input); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa.cpp:280:47: required from here 280 | auto result = lexy::parse(lexy::string_input(line, len), lexy_ext::report_error); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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]}; | ^~~ [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 40%] 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_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_recorder.c [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_red_black.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_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 [ 41%] 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 [ 41%] 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 [ 41%] 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/io_base.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:10: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, 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/io/binary/graph.hpp:12: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 41%] 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 [ 41%] 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 [ 41%] 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 [ 42%] 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 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]' 108 | DeleteLink(graph_.conjugate(w), graph_.conjugate(in_edge)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/graph/gfa_reader.cpp:185:25: required from here 185 | helper.LinkEdges(e1, e2); | ~~~~~~~~~~~~~~~~^~~~~~~~ /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 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 42%] 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 [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o [ 42%] 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/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 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 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 [ 43%] 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 [ 43%] 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 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__ | ^~~~~~ [ 43%] 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 [ 43%] 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/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 [ 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/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 [ 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 [ 45%] 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 [ 45%] 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 [ 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/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 [ 45%] 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 [ 45%] 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 [ 46%] 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_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 [ 47%] 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 [ 47%] 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); | ^~~~~~~~ [ 48%] 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 [ 48%] 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 [ 48%] 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 [ 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/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 [ 48%] 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_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 [ 48%] 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] 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 /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' [ 48%] 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 [ 48%] Built target samtools [ 48%] 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 [ 48%] 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 [ 48%] 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 [ 48%] 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 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' [ 48%] 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 [ 48%] 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 [ 50%] 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 [ 50%] 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 [ 50%] 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 [ 51%] 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 -fstack-clash-protection -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 [ 51%] 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 /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' [ 51%] Built target bwa [ 51%] 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 [ 51%] 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 [ 51%] 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 [ 51%] 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 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=" 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 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' [ 51%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/main.c.o [ 51%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/fastmap.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 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 [ 51%] 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 -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_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_threads.c [ 51%] Building C object ext/easel/CMakeFiles/easel.dir/esl_varint.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_varint.c.o -MF CMakeFiles/easel.dir/esl_varint.c.o.d -o CMakeFiles/easel.dir/esl_varint.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_varint.c [ 51%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.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_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_tree.c [ 51%] 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 [ 51%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.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_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 /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' [ 51%] Built target binary_io [ 51%] 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 [ 52%] 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 [ 53%] 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 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', inlined from 'cmd2argv' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:246:2, inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:100:10: warning: '__builtin_strncpy' specified bound between 18446744071562067969 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 100 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'cmd2argv', inlined from 'kopen' at /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:307:13: /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:245:32: warning: argument 1 range [18446744071562067970, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 245 | argv[0] = str = (char*)calloc(end - beg + 1, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/kopen.c:7: /usr/include/stdlib.h: In function 'kopen': /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) | ^~~~~~ [ 53%] Linking CXX static library libgraphio.a [ 53%] 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/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake [ 53%] 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/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 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/bwtaln.c.o -MF CMakeFiles/spades-bwa.dir/bwtaln.c.o.d -o CMakeFiles/spades-bwa.dir/bwtaln.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtaln.c [ 53%] 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 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 [ 53%] 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 [ 53%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwaseqio.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 /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' [ 53%] Built target graphio 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/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=" [ 53%] 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 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' [ 53%] 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 [ 53%] 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 [ 53%] 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/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 [ 54%] 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 -I/build/reproducible-path/spades-4.0.0+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_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 [ 54%] 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 -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 [ 54%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.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/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 [ 54%] 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/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 /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_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/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 [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o [ 56%] 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/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 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/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 [ 57%] 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 -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwase.c.o -MF CMakeFiles/spades-bwa.dir/bwase.c.o.d -o CMakeFiles/spades-bwa.dir/bwase.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwase.c [ 57%] 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 [ 57%] 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 /usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alloc.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_arr2.c.o CMakeFiles/easel.dir/esl_arr3.c.o CMakeFiles/easel.dir/esl_bitfield.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_cpu.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o 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CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_subcmd.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_varint.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_avx512.c.o CMakeFiles/easel.dir/esl_neon.c.o /usr/bin/ranlib libeasel.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 57%] Built target easel make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+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' [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o [ 58%] 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 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 [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o [ 58%] 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 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 [ 58%] 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 [ 58%] 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/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o [ 59%] Linking CXX static library libllvm-support.a 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/generic_decoding.c.o -MF CMakeFiles/hmmer.dir/src/generic_decoding.c.o.d -o CMakeFiles/hmmer.dir/src/generic_decoding.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_decoding.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 [ 59%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-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/generic_fwdback.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback.c [ 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 -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/generic_fwdback_chk.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback_chk.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o [ 60%] 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 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/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 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/generic_null2.c.o -MF CMakeFiles/hmmer.dir/src/generic_null2.c.o.d -o CMakeFiles/hmmer.dir/src/generic_null2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_null2.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.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/generic_msv.c.o -MF 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 /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/generic_optacc.c.o -MF CMakeFiles/hmmer.dir/src/generic_optacc.c.o.d -o CMakeFiles/hmmer.dir/src/generic_optacc.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_optacc.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_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/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_stotrace.c [ 62%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-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/generic_viterbi.c.o -MF CMakeFiles/hmmer.dir/src/generic_viterbi.c.o.d -o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_viterbi.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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 62%] Building C object 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/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/h2_io.c.o -MF CMakeFiles/hmmer.dir/src/h2_io.c.o.d -o CMakeFiles/hmmer.dir/src/h2_io.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/h2_io.c [ 62%] Built target samio [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o [ 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 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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/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 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' 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=" /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' [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o [ 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 -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 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/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 [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o 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 [ 63%] Built target llvm-support 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/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/modelconfig.c.o make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend 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 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' 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=" 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/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/modelconfig.c 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 [ 63%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.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/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/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 [ 63%] 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 [ 63%] 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 [ 63%] 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 /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' [ 64%] 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 [ 64%] Built target spades-bwa [ 64%] 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/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 [ 64%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.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 [ 65%] 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 [ 67%] 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 [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/reproducible-path/spades-4.0.0+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 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); | ^~~~~~ [ 67%] 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/__/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 [ 67%] 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 [ 67%] 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 /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/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 [ 67%] 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 /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/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 /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], | ^~~~~~ [ 67%] 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 /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_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_alidisplay.c [ 67%] 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/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 [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.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_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 [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.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_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_builder.c [ 67%] 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 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 | } | ^ 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: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/14/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' 1018 | _M_erase_at_end(this->_M_impl._M_start + __new_size); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map.hpp:166:21: required from 'void kmers::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' 166 | data_.resize(sz); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:31:21: required from 'kmers::KMerDiskStorage kmers::PerfectHashMapBuilder::BuildIndex(kmers::PerfectHashMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = kmers::InvertableStoring; Counter = kmers::KMerDiskCounter >; typename Counter::Seq = RuntimeSeq<128>; size_t = long unsigned int]' 31 | index.resize(res.total_kmers()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/ph_map/perfect_hash_map_builder.hpp:140:39: required from 'void kmers::BuildIndex(PerfectHashMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmer_index_traits >; StoringType = InvertableStoring; Counter = KMerDiskCounter >; size_t = long unsigned int]' 140 | PerfectHashMapBuilder().BuildIndex(index, counter, bucket_num, thread_num, save_final); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/index/edge_index_builders.hpp:280:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&, fs::impl::TmpDir, size_t) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' 280 | BuildIndex(index, counter, 10 * nthreads, nthreads); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:29:43: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&, bool) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' 29 | IndexBuilder().BuildIndexFromGraph(index, g, fs::tmp::make_temp_dir(workdir_, "edge_index")); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/edge_index_refiller.cpp:36:70: required from here 36 | void EdgeIndexRefiller::Refill(EdgeIndex &index, const Graph &g, bool); | ^ /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_; | ^~~~~~~~ [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.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_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_domaindef.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.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_gbands.c.o -MF CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gbands.c [ 68%] 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 [ 68%] 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 [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmx.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmx.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmx.c [ 68%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.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_gmxb.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_gmxb.c [ 68%] Building C object 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 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-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 [ 68%] 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 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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/p7_hmmfile.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmfile.c [ 69%] 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 [ 69%] 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 -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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-ffile-prefix-map=/build/reproducible-path/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_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_pipeline.c [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.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_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_prior.c [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.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_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_profile.c [ 70%] 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 [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.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_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_spensemble.c [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.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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/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' [ 70%] Built target toolchain [ 70%] 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 -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_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_trace.c [ 70%] 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 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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 [ 71%] 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 -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_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 [ 71%] 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 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ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o -MF CMakeFiles/hmmer.dir/src/p7_domain.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domain.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_domain.c [ 71%] 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 [ 71%] 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 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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 [ 71%] 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 [ 71%] 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 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ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_sse.c [ 73%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.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_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/fm_ssv.c [ 73%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/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 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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 [ 73%] 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 [ 73%] 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 && 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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 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 [ 74%] 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 [ 74%] 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 [ 74%] 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 [ 74%] 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 [ 75%] 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 [ 75%] 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 [ 76%] 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 /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' [ 76%] 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' [ 76%] 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_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 [ 76%] Building CXX object common/library/CMakeFiles/library.dir/library.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 [ 76%] 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' [ 76%] 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' [ 76%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o [ 76%] 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 /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; | ~~~~^ [ 76%] 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' [ 76%] 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' [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o [ 76%] 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/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/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 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/repeat_resolving.cpp.o [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.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 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 [ 78%] 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/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 [ 78%] 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/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 [ 79%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-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 [ 79%] 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/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 [ 79%] 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/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 /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()); | ^~~~ [ 79%] 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 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; | ^~~~~~~ [ 79%] Linking CXX static library liblibrary.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -P CMakeFiles/library.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/library && /usr/bin/cmake -E cmake_link_script CMakeFiles/library.dir/link.txt --verbose=1 /usr/bin/ar qc liblibrary.a CMakeFiles/library.dir/library.cpp.o CMakeFiles/library.dir/library_data.cpp.o /usr/bin/ranlib liblibrary.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 79%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.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/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=" [ 79%] 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 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' [ 79%] 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 /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/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/sequence_mapper_notifier.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:11: /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:434:46: required from here 434 | omnigraph::CompressAllVertices(g_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /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()); | ^~~ [ 80%] 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 [ 80%] 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/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 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/projects/spades/hybrid_aligning.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp:9: /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /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/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: /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/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 { | ^~~~ /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/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], | ^~~~~~ [ 80%] 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 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 [ 80%] 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/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 /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) { | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': /build/reproducible-path/spades-4.0.0+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()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 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 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 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, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:8: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp: In member function 'omnigraph::MappingPath alignment::BWAIndex::GetMappingPath(const mem_alnreg_v&, const Sequence&, bool) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:29: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'long unsigned int' [-Wformat=] 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | i, 337 | pos, pos + a.re - a.rb, a.qb, a.qe, | ~~~~~~~~~~~~~~~~~ | | | long unsigned int /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/logger/logger.hpp:152:13: note: in definition of macro 'LOG_EXPR' 152 | expr; \ | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:331:9: note: in expansion of macro 'DEBUG_EXPR' 331 | DEBUG_EXPR({ | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/bwa_index.cpp:335:44: note: format string is defined here 335 | fprintf(stderr, "%zu: [%zu, %lld)\t[%d, %d) %c %ld %s %d %d\n", | ~~~^ | | | long long int | %ld [ 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 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 [ 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 [ 81%] 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 [ 81%] 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 [ 82%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_filler.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 [ 82%] Building CXX object common/alignment/CMakeFiles/alignment.dir/pacbio/gap_dijkstra.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_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 /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_mapper.cpp:280:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 280 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ 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]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.cpp:18:41: required from here 18 | Sequence merged_seq = MergeSequences(g_, path); | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp:120:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 120 | auto end = g.EdgeEnd(continuous_path[i - 1]); | ^~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_dijkstra.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/pacbio/gap_filler.hpp: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': /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 | } | ^ [ 82%] 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/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 [ 82%] 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 /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' [ 82%] 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 /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.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 [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.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_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/loop_traverser.cpp [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.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/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 [ 82%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+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 In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp:9: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 82%] Building CXX object 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/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pe_resolver.cpp [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.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 [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.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 /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/path_extenders.cpp: In member function 'bool path_extend::LoopDetectingPathExtender::TryToResolveHairpin(path_extend::BidirectionalPath&)': /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]; | ^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:9: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15, 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/common/assembly_graph/stats/picture_dump.hpp:13: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.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/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 [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.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 [ 84%] 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/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 [ 84%] Linking CXX static library libalignment.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 [ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.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.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 [ 85%] 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/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 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/gap_info.cpp.o CMakeFiles/alignment.dir/bwa_index.cpp.o CMakeFiles/alignment.dir/long_read_mapper.cpp.o CMakeFiles/alignment.dir/sequence_mapper_notifier.cpp.o CMakeFiles/alignment.dir/kmer_sequence_mapper.cpp.o CMakeFiles/alignment.dir/pacbio/gap_filler.cpp.o CMakeFiles/alignment.dir/pacbio/gap_dijkstra.cpp.o CMakeFiles/alignment.dir/pacbio/g_aligner.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 85%] Built target alignment [ 85%] 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/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 [ 85%] 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/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 /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_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.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/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 make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+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=" 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' [ 85%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.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 /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_) { | ^~~~~~~~~~~~~~~ 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, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/pipeline/launcher.cpp:12: /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], | ^~~~~~ [ 86%] 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 [ 86%] 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/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 /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/stacktrace.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/verify.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/binary.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment/long_read_storage.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.hpp:11: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /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/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/modules/chromosome_remover.hpp:8, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/chromosome_remover.cpp:6: /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/common/modules/chromosome_remover.cpp:40:58: required from here 40 | 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()); | ^~~ /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/common/modules/chromosome_remover.cpp:137:64: required from here 137 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { | ^~~~ /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/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 633 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { | ^~~~~~~~~~~ /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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 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' [ 86%] Built target spades-stages [ 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 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/sequence_mapper_gp_api.cpp.o [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o [ 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/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/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/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 [ 86%] Linking CXX static library libmodules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.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]': /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], | ^~~~~~ /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/path_extend/scaff_supplementary.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+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[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 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 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 [ 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/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/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 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/paired_info/split_path_constructor.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, false, long unsigned int>]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/split_path_constructor.hpp:104:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' 104 | std::vector common_part = GetCommonPathsEnd(graph_, cur_edge, cur_info.second, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 | (size_t) (cur_info.d() - cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 | (size_t) (cur_info.d() + cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 | dijkstra); | ~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:176:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 176 | auto paths = spc.ConvertPIToSplitPaths(e, index_, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 177 | lib_.data().mean_insert_size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 | lib_.data().insert_size_deviation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:63:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 63 | missing_paired_info_count = FillMissing(nthreads); | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/pair_info_improver.hpp:54:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 54 | CorrectPairedInfo(num_threads); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:144:94: required from here 144 | PairInfoImprover(graph, clustered_index, lib, max_repeat_length).ImprovePairedInfo(omp_get_max_threads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /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, | ~~~~~~~^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/index_point.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/histogram.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info_buffer.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/distance_estimation_utils.cpp:8: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'omnigraph::de::PairedIndex::~PairedIndex()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:26:7, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = omnigraph::de::PairedIndex; _Tp = omnigraph::de::PairedIndex]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'void std::__relocate_object_a(_Tp*, _Up*, _Allocator&) [with _Tp = omnigraph::de::PairedIndex; _Up = omnigraph::de::PairedIndex; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1076:24, inlined from '_ForwardIterator std::__relocate_a_1(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1103:26, inlined from '_ForwardIterator std::__relocate_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = omnigraph::de::PairedIndex*; _ForwardIterator = omnigraph::de::PairedIndex*; _Allocator = allocator >]' at /usr/include/c++/14/bits/stl_uninitialized.h:1145:33, inlined from 'static std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_S_relocate(pointer, pointer, pointer, _Tp_alloc_type&) [with _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/stl_vector.h:509:26, inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]' at /usr/include/c++/14/bits/vector.tcc:647:32: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:17: /usr/include/parallel_hashmap/btree.h: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {const debruijn_graph::DeBruijnGraph&}; _Tp = omnigraph::de::PairedIndex; _Alloc = std::allocator >]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 86%] 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 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/graph_pack.cpp.o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o CMakeFiles/pipeline.dir/stage.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-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/common/stages /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/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.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/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 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' [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.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/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/genomic_info_filler.cpp [ 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 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 [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o [ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/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 cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.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/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/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=16777216UL -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 [ 89%] 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/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 /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; | ~~~~~~~~~~^~ [ 90%] 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=16777216UL -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 [ 90%] 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=16777216UL -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 /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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:93:63: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 93 | transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:104:45: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 104 | int num_flows = read.raw_measurements.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:134:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 134 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:173:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 173 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:357:38: warning: conversion from 'double' to 'float' changes value from '1.0e+20' to '1.00000002e+20f' [-Wfloat-conversion] 357 | float sum_of_squares_upper_bound = 1e20; //max_flows; // Squared distance of solution to measurements | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/seqeval/TreephaserLite.cpp:416:35: warning: conversion from 'double' to 'float' changes value from '-1.0000000000000001e-1' to '-1.00000001e-1f' [-Wfloat-conversion] 416 | float max_per_flow_metric = -0.1; | ^~~~ /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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/reference.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 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: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp: In instantiation of 'static size_t hammer::HSeq::GetDataSize(size_t) [with long unsigned int N = 16; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:174:52: required from 'void kmers::KMerDiskStorage::merge() [with S = hammer::HSeq<16>; traits = kmers::kmer_index_traits >]' 174 | BucketStorage bucket(*entry, Seq::GetDataSize(k_), false); | ~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_index_builder.hpp:461:25: required from 'auto kmers::KMerIndexBuilder::BuildIndex(Index&, kmers::KMerCounter&, bool) [with Index = kmers::KMerIndex > >; typename Index::KMerSeq = hammer::HSeq<16>]' 461 | kmer_storage.merge(); | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/kmer_data.cpp:173:102: required from here 173 | auto res = kmers::KMerIndexBuilder(num_files_, cfg::get().max_nthreads).BuildIndex(data.index_, counter, false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/HSeq.hpp:94:36: warning: unused parameter 'size' [-Wunused-parameter] 94 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 90%] 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=16777216UL -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 [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_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=16777216UL -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 [ 92%] 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 [ 92%] 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=16777216UL -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 /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' [ 92%] Built target paired_info 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/graph_support/graph_processing_algorithm.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:12: /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/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = adt::identity; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:349:94: required from here 349 | SelfConjugateDisruptor(g_, cfg::get().max_repeat_length, removal_handler_).Run(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /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::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(); | ~~~~~~~~~~^~ /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:366:28: required from here 366 | cov_cleaner.Run(); | ~~~~~~~~~~~~~~~^~ /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::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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:487:24: required from here 487 | CompressAllVertices(gp.get_mutable()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /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(); | ~~~~~~~~~~^~ /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 = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:85:52: required from here 85 | bool changed = TopologyRemoveErroneousEdges(g_, simplif_cfg_.tec, handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:95:33: required from 'omnigraph::GraphComponent omnigraph::ComplexTipFinder::operator()(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 95 | if (finder.FillDominated()) { | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_tip_clipper.hpp:150:49: required from 'omnigraph::ComplexTipClipper::ComplexTipClipper(Graph&, double, size_t, size_t, size_t, const std::filesystem::__cxx11::path&, HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 150 | [&](VertexId v) {return !finder_(v).empty();}, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function, std::allocator >&)>&}; _Tp = omnigraph::ComplexTipClipper]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], function, allocator >&)>&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::ComplexTipClipper]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:501:65: required from 'omnigraph::AlgoPtr debruijn::simplification::ComplexTipClipperInstance(Graph&, debruijn_graph::config::debruijn_config::simplification::complex_tip_clipper, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 501 | return std::make_shared>(g, ctc_conf.max_relative_coverage, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | ctc_conf.max_edge_len, | ~~~~~~~~~~~~~~~~~~~~~~ 503 | parser.max_length_bound(), info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 504 | "", removal_handler); | ~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:268:42: required from here 268 | ComplexTipClipperInstance(g_, simplif_cfg_.complex_tc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 /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: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; typename enable_if<(! is_array<_Tp>::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:257:57: required from here 257 | RelativeCoverageComponentRemoverInstance(g_, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 258 | simplif_cfg_.rcc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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/stages/simplification.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]': /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/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/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]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/main.cpp:91:3: warning: control reaches end of non-void function [-Wreturn-type] 91 | } | ^ [ 92%] Linking CXX executable ../../bin/spades-ionhammer cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.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-ionhammer.dir/link.d "CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o" "CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o" "CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o" "CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o" "CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o" "CMakeFiles/spades-ionhammer.dir/main.cpp.o" "CMakeFiles/spades-ionhammer.dir/reference.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o" "CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o" "CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o" "CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o" "CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-ionhammer ../../common/modules/libmodules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/kmer_index/libmph_index.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/alignment/libalignment.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../common/modules/path_extend/libpath_extend.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 -lssw ../../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 ../../_deps/zlib_ng-build/libz.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target spades-ionhammer In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/pack.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/stage.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification.cpp:9: 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingConstAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:567:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'void std::__new_allocator<_Tp>::destroy(_Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/new_allocator.h:198:13, inlined from 'static void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:597:15, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingConstAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [ 92%] Linking CXX static library libstages.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -E cmake_link_script CMakeFiles/stages.dir/link.txt --verbose=1 /usr/bin/ar qc libstages.a CMakeFiles/stages.dir/read_conversion.cpp.o CMakeFiles/stages.dir/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o CMakeFiles/stages.dir/ss_edge_split.cpp.o CMakeFiles/stages.dir/genomic_info_filler.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.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 /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 /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /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/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -MF CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d -o CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/concurrent_dsu.cpp [ 92%] Linking CXX static library libcommon_modules.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common && /usr/bin/cmake -E cmake_link_script CMakeFiles/common_modules.dir/link.txt --verbose=1 /usr/bin/ar qc libcommon_modules.a CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o /usr/bin/ranlib libcommon_modules.a 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 -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' 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-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' make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.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/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[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[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[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-gsimplifier.dir/DependInfo.cmake "--color=" 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-read-filter.dir/DependInfo.cmake "--color=" 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]: 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-gbuilder.dir/build.make projects/spades_tools/CMakeFiles/spades-gbuilder.dir/build make[4]: Leaving 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/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]: 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 projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build 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' 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 projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.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]: 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 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]: Leaving 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 make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build 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' 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[4]: Entering 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 -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' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.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 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-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/convert_bin_to_fasta.cpp [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.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/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_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 [ 95%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o [ 96%] Building CXX object projects/spades_tools/CMakeFiles/spades-gbuilder.dir/gbuilder.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 [ 96%] 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++ -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-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 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 [ 96%] 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/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 [ 96%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 96%] 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/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/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 [ 96%] Building CXX object 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/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 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/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 [ 96%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.cpp.o [ 96%] 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 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 [ 97%] 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/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 /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; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/pipeline.cpp: In function 'void spades::assemble_genome()': /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, | ~~~~~~~~~~~^ 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] 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/projects/spades_tools/gbuilder.cpp:25: /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], | ^~~~~~ [ 97%] 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 [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.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/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.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/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/dataset_processor.cpp In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:36, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/sequence.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/single_read.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/reads/io_helper.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:14: In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4755:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4785:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 48 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4785:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 56 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4755:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4786:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 'const xxh_unalign64 {aka const long unsigned int}[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [33, 40] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4786:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset [41, 48] into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'xxh_u64 XXH_read64(const void*)', inlined from 'xxh_u64 XXH_readLE64(const void*)' at /usr/include/xxhash.h:3425:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /usr/include/xxhash.h:4756:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:4788:35, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /usr/include/xxhash.h:6175:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /usr/include/xxhash.h:6201:32, inlined from 'static size_t RuntimeSeq::GetHash(const DataType*, size_t, uint64_t) [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:691:36, inlined from 'size_t RuntimeSeq::GetHash(uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:695:23, inlined from 'size_t RuntimeSeq::hash::operator()(const RuntimeSeq&, uint64_t) const [with long unsigned int max_size_ = 128; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:700:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_buckets.hpp:51:22, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/kmer_index/kmer_mph/kmer_splitter.hpp:116:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:79:51: /usr/include/xxhash.h:3356:39: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 3356 | return *((const xxh_unalign64*)ptr); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/kmercount.cpp:76:17: note: at offset 40 into object 'kmer' of size 40 76 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ /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)) { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/contig_processor.cpp:162:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {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)) { | ~~~~~~~~~~~~~~^~ 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/bwa_index.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/compressor.hpp:130:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 130 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_gap_closer.hpp:752:28: required from here 752 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /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()); | ^~~ [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 97%] 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 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/gmapper.cpp:19: /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/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(); | ^~~~~~~~~~~~~~~ [ 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/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/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/corrector/config_struct.cpp [ 97%] 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 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: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools/simplification.hpp:157:65: required from here 157 | algo.AddAlgo(RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 158 | rcc_config(rel_cov_proc_enabled), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | simplif_info, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~ /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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 97%] Built target spades-convert-bin-to-fasta [ 97%] 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 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/projects/spades_tools/gsimplifier.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]': /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/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/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/stages/simplification_pipeline/graph_simplification.hpp:11: /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(); | ~~~~~~~~~~^~ /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /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 = 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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /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::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(); | ~~~~~~~~~~^~ /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /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()); | ^~~ [ 97%] 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 [ 97%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 97%] 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 /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' [ 97%] Built target spades-kmer-estimating [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/kmer_cluster.cpp [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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/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 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:544:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' 544 | vm.Start(vals, num_elems, num_threads); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:55:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' 55 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/hamcluster.cpp:148:21: required from here 148 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | if (sz < block_thr) { | ~~~~~~~~~~~~~~~~~~~~~ 150 | // Merge small blocks. | ~~~~~~~~~~~~~~~~~~~~~~ 151 | processBlockQuadratic(uf, start, sz, data, tau_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 | } else { | ~~~~~~~~ 153 | big_blocks1 += 1; | ~~~~~~~~~~~~~~~~~ 154 | // Otherwise - dump for next iteration. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 | for (unsigned i = 0; i < tau_ + 1; ++i) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 | serialize(bfs, kfs, | ~~~~~~~~~~~~~~~~~~~ 157 | data, &start, sz, | ~~~~~~~~~~~~~~~~~ 158 | SubKMerStridedSerializer(i, tau_ + 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | } | ~ 160 | } | ~ 161 | }); | ~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/parallel_radix_sort.hpp:401:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 401 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ [ 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 [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 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 /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 [ 98%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 [ 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 [ 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/hammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -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 /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/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); | ^~~~~~~~~~ [ 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/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 /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp: In function 'void CheckGFAInOut(const std::string&, const std::string&, const std::filesystem::__cxx11::path&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:63:17: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 63 | Graph graph(K); | ^ /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/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()); | ^~~ /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); | ^ /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, std::__cxx11::basic_string > >&, size_t, size_t, const std::vector >&, const CoverageInfo&, const EdgePairInfo&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/test_utils.cpp:193:30: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 193 | graph_pack::GraphPack gp(k, "tmp", 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/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/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.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::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/io_test.cpp:51:38: required from here 51 | for (size_t i = 0; i < 5; ++i, ++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/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:91:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 91 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:103:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 103 | gap_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:114:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 114 | ends_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:142:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 142 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:152:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 152 | if (g.int_id(e) == eid_int) { | ~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:173:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 173 | Graph g(K); | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graph_alignment_test.cpp:182:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 182 | if (g.int_id(e) == eid_int) { | ~~~~~~~~~~~~^~~~~~~~~~ /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/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/io_test.cpp:38:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' 38 | ++it1; | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:95:26: required from here 95 | CompareGraphIterators(graph.SmartEdgeBegin(), new_graph.SmartEdgeBegin()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 { | ~~~~~~~^~~~~~~~ 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/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/stages/simplification_pipeline/graph_simplification.hpp:11, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:12: /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:276:16: required from here 276 | remover.Run(); | ~~~~~~~~~~~^~ /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(); | ~~~~~~~~~~^~ /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 = omnigraph::LengthComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:60:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 60 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:45:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 45 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:63:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 63 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:223:72: required from here 223 | while(debruijn::simplification::TopologyRemoveErroneousEdges(g, tec_config, 0)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /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/test/debruijn/random_graph.hpp:12, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/paired_info_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::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/random_graph.hpp:49:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 49 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:174:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' 174 | this->value_.Remove(this->GetRandomEdge()); | ~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:185:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' 185 | RemoveRandomEdgeInfo(); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:177:10: required from here 177 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /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::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/random_graph.hpp:41:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 41 | ++it; | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:101:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' 101 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:120:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' 120 | AddRandomEdge(); | ^~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/random_graph.hpp:113:10: required from here 113 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /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/modules/simplification/chimera_stats.hpp:13, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:12: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:85:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 85 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:506:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 506 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:669:49: required from 'std::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 669 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/relative_coverage_remover.hpp:722:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::filesystem::__cxx11::path) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>]' 722 | [&](EdgeId e) { return static_cast(finder_(e)); }, chunk_cnt); | ~~~~~~~^~~ /usr/include/c++/14/bits/stl_construct.h:119:7: required from 'constexpr void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:706:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/14/bits/shared_ptr_base.h:969:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 969 | auto __pi = ::new (__mem) | ^~~~~~~~~~~~~ 970 | _Sp_cp_type(__a._M_a, std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr_base.h:1713:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' 1713 | : _M_ptr(), _M_refcount(_M_ptr, __tag, std::forward<_Args>(__args)...) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/shared_ptr.h:463:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::filesystem::__cxx11::path&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 463 | : __shared_ptr<_Tp>(__tag, std::forward<_Args>(__args)...) | ^ /usr/include/c++/14/bits/shared_ptr.h:1007:14: required from 'std::shared_ptr > std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, filesystem::__cxx11::path&}; _NonArray<_Tp> = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' 1007 | return shared_ptr<_Tp>(_Sp_alloc_shared_tag<_Alloc>{__a}, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1008 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:438:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' 437 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 439 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 440 | flanking_cov, | ~~~~~~~~~~~~~ 441 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 442 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 443 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 445 | max_coverage, | ~~~~~~~~~~~~~ 446 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/simplification_test.cpp:313:83: required from here 313 | auto algo = debruijn::simplification::RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 314 | standard_rcc_config(), | ~~~~~~~~~~~~~~~~~~~~~~ 315 | standard_simplif_relevant_info()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/path_extend_test.cpp:9: /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/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': /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 | } | ^ 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(); | ~~~~~~~~~~^~ /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:378:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 378 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/graph_support/parallel_processing.hpp:354:12: required from here 354 | size_t Run(bool force_primary_launch = false, | ^~~ /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/modules/simplification/complex_tip_clipper.hpp:14, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/dominated_set_finder.hpp:107:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 107 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:989:43: required from 'omnigraph::complex_br::LocalizedComponentFinder::LocalizedComponentFinder(const Graph&, size_t, size_t, VertexId) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; VertexId = omnigraph::impl::VertexId]' 989 | dominated_set_finder.FillDominated(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1058:41: required from 'bool omnigraph::complex_br::CandidateFinder::Check(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1058 | LocalizedComponentFinder comp_finder(g, max_length_, | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1056:10: required from here 1056 | bool Check(VertexId v) const override { | ^~~~~ /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 { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 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/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 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]' 812 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:776:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 776 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'omnigraph::complex_br::ComponentProjector::EdgeId omnigraph::complex_br::ComponentProjector::CorrespondingTreeEdge(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:823:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 823 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:792:16: warning: unused variable 'end_height' [-Wunused-variable] 792 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /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 = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 252 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:821:43: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 821 | gc.e_end()); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1120:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1120 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1147:17: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::InnerProcess(VertexId, std::vector&) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId; typename Graph::VertexId = omnigraph::impl::VertexId]' 1147 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1193:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1193 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:1187:10: required from here 1187 | bool Process(VertexId v) override { | ^~~~~~~ /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/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:10: required from here 310 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:310:32: warning: unused parameter 'v' [-Wunused-parameter] 310 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:321:10: required from here 321 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:323:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 323 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::ComponentColoring::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:18: required from here 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:477:71: warning: unused parameter 'edge2' [-Wunused-parameter] 477 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here 242 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/simplification/complex_bulge_remover.hpp:245:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 245 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ 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 /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/graphio.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/debruijn/io_test.cpp:8: 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 'constexpr void std::allocator< >::deallocate(_Tp*, std::size_t) [with _Tp = phmap::priv::Deallocate<8, std::allocator > > > > >(std::allocator > > > >*, void*, size_t)::M]' at /usr/include/c++/14/bits/allocator.h:208:35, 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, inlined from 'void phmap::priv::btree::deallocate(size_type, node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2003:60, inlined from 'void phmap::priv::btree::delete_leaf_node(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2013:23, inlined from 'void phmap::priv::btree::internal_clear(node_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:3228:29, inlined from 'void phmap::priv::btree::clear() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2859:27, inlined from 'phmap::priv::btree::~btree() [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:1704:18, inlined from 'phmap::priv::btree_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_container()' at /usr/include/parallel_hashmap/btree.h:3264:11, inlined from 'phmap::priv::btree_set_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_set_container()' at /usr/include/parallel_hashmap/btree.h:3429:11, inlined from 'phmap::priv::btree_map_container > >, phmap::Less, std::allocator > > > >, 256, false> > >::~btree_map_container()' at /usr/include/parallel_hashmap/btree.h:3591:11, inlined from 'phmap::btree_map > >, phmap::Less, std::allocator > > > > >::~btree_map()' at /usr/include/parallel_hashmap/btree.h:3952:15, inlined from 'omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >::~NoLockingAdapter()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/paired_info.hpp:536:7, inlined from 'std::pair > >, phmap::Less, std::allocator > > > > > > >::~pair()' at /usr/include/c++/14/bits/stl_pair.h:284:12, inlined from 'constexpr void std::destroy_at(_Tp*) [with _Tp = pair > >, phmap::Less, allocator > > > > > > >]' at /usr/include/c++/14/bits/stl_construct.h:88:18, inlined from 'static constexpr void std::allocator_traits >::destroy(allocator_type&, _Up*) [with _Up = std::pair > >, phmap::Less, std::allocator > > > > > > >; _Tp = std::pair > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/c++/14/bits/alloc_traits.h:599:19, inlined from 'static decltype (std::allocator_traits::destroy(a, p)) phmap::allocator_traits::destroy_impl(int, A&, T*) [with A = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1546:42, inlined from 'static void phmap::allocator_traits::destroy(Alloc&, T*) [with T = std::pair > >, phmap::Less, std::allocator > > > > > > >; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:1504:21, inlined from 'static void phmap::priv::map_slot_policy::swap(Allocator*, slot_type*, slot_type*) [with Allocator = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; K = omnigraph::impl::EdgeId; V = omnigraph::de::NoLockingAdapter > >, phmap::Less, std::allocator > > > > > >]' at /usr/include/parallel_hashmap/phmap_base.h:4554:56, inlined from 'static void phmap::priv::common_params::swap(Alloc*, slot_type*, slot_type*) [with Key = omnigraph::impl::EdgeId; Compare = phmap::Less; Alloc = std::allocator > >, phmap::Less, std::allocator > > > > > > > >; int TargetNodeSize = 256; bool Multi = false; SlotPolicy = phmap::priv::map_slot_policy > >, phmap::Less, std::allocator > > > > > > >]' at /usr/include/parallel_hashmap/btree.h:888:30, inlined from 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]' at /usr/include/parallel_hashmap/btree.h:2382:30: /usr/include/c++/14/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on unallocated object 'empty_node' [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/adt/queue_iterator.hpp:15: /usr/include/parallel_hashmap/btree.h: In function 'void phmap::priv::btree_node::swap(phmap::priv::btree_node*, allocator_type*) [with Params = phmap::priv::map_params > >, phmap::Less, std::allocator > > > > > >, phmap::Less, std::allocator > >, phmap::Less, std::allocator > > > > > > > >, 256, false>]': /usr/include/parallel_hashmap/btree.h:1623:44: note: declared here 1623 | static constexpr EmptyNodeType empty_node( | ^~~~~~~~~~ [100%] Linking CXX executable ../../bin/debruijn_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/cmake -E cmake_link_script CMakeFiles/debruijn_test.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/debruijn_test.dir/link.d CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o CMakeFiles/debruijn_test.dir/test_utils.cpp.o CMakeFiles/debruijn_test.dir/construction_test.cpp.o CMakeFiles/debruijn_test.dir/io_test.cpp.o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o CMakeFiles/debruijn_test.dir/graphio.cpp.o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o CMakeFiles/debruijn_test.dir/v_overlaps.cpp.o CMakeFiles/debruijn_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/debruijn_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/graph/libgraphio.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../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 -lm ../../_deps/zlib_ng-build/libz.a ../../ext/lexy/src/liblexy_file.a make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target debruijn_test make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/Makefile2 include_test make[3]: 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 42 make -f CMakeFiles/Makefile2 test/include_test/CMakeFiles/include_test.dir/all 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 -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 -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/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/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 -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/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[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[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/src/common/modules/coverage_model /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' 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/ext/src/zlib-ng /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu 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&& /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[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 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'/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[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[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' 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 [ 2%] Built target mimalloc-obj [ 2%] Built target gqf [ 4%] Built target mph_index [ 4%] Built target edlib [ 4%] Built target format make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 7%] Built target teamcity_gtest [ 7%] Built target coverage_model [ 9%] Built target binary_io make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 11%] Built target version 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 [ 30%] 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' 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 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' 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/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[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 [ 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 '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]: 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 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' 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 ext/bwa/CMakeFiles/bwa.dir/build.make ext/bwa/CMakeFiles/bwa.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' [ 52%] Built target sequence [ 54%] Built target utils [ 64%] Built target samtools make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make -f common/io/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=" [ 71%] 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=" 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 'common/io/sam/CMakeFiles/samio.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/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+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' [ 71%] 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=" [ 73%] 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=" 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' 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 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' [ 78%] 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=" [ 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=" 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' 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]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 80%] 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=" [ 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]: 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[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[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]: 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 [ 85%] Built target configs 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/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.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]: 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 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' [ 92%] 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' 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/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/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 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' 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/stages /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/stages /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[5]: 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[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target stages make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_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 /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 /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_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/CMakeFiles/common_modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target common_modules make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.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/test/include_test /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/test/include_test /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test/CMakeFiles/include_test.dir/DependInfo.cmake "--color=" 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' [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o [ 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/binary_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/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 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/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/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/quality_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/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/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 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, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:157:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:156:12: note: 's1$_M_elems$' was declared here 156 | Seq<7> s1("ACGTACT"); | ^~ 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, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:160:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:68: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:159:12: note: 's2$_M_elems$' was declared here 159 | Seq<7> s2("TTTTTTT"); | ^~ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftLeft_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:28:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftLeft_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:27:13: note: 's$_M_elems$' was declared here 27 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'Seq Seq::operator>>(char) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'virtual void Seq_ShiftRight_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:41:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:342:42: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 342 | res.data_[i] = (res.data_[i] << 2) | rm; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftRight_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:40:13: note: 's$_M_elems$' was declared here 40 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void Seq_Str_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:55:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Str_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:54:13: note: 's$_M_elems$' was declared here 54 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_HeadAndTail_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:62:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_HeadAndTail_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:61:13: note: 's$_M_elems$' was declared here 61 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:138:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:137:13: note: 's$_M_elems$' was declared here 137 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'void Seq::set(size_t, char) [with long unsigned int size_ = 9; T = long unsigned int]', inlined from 'Seq Seq::operator!() const [with long unsigned int size_ = 9; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:241:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:142:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:358:40: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 358 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:141:12: note: 's3$_M_elems$' was declared here 141 | Seq<9> s3("ACGTACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<10>; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'virtual void Seq_FromBiggerSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:68:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_FromBiggerSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:67:13: note: 's$_M_elems$' was declared here 67 | Seq<10> s("ACGTACGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::end() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:445:16, inlined from 'virtual void Seq_End_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:116:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_End_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:115:12: note: 's1$_M_elems$' was declared here 115 | Seq<5> s1("ACGTA"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'Seq::Seq(const S&, size_t, size_t, bool) [with S = Seq<5>; long unsigned int size_ = 4; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:200:35, inlined from 'Seq Seq::start() const [with long unsigned int size2_ = 4; T2 = long unsigned int; long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:439:16, inlined from 'virtual void Seq_Start_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:121:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Start_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:120:12: note: 's1$_M_elems$' was declared here 120 | Seq<5> s1("ACGTA"); | ^~ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 4; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:80:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:79:16: note: 's$_M_elems$' was declared here 79 | Seq<4> s("ACGT"); | ^ In file included from /usr/include/gtest/gtest.h:71, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:13: /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:84:38: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 84 | EXPECT_EQ("ACGTC", s.pushBack('C').str()); | ~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:83:31: note: 's$_M_elems$' was declared here 83 | Seq<4, unsigned char> s("ACGT"); | ^ In member function 'Seq<(size_ + 1), T> Seq::pushBack(char) const [with long unsigned int size_ = 3; T = long unsigned int]', inlined from 'virtual void Seq_PushBack_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:88:9: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:288:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 288 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:87:16: note: 's$_M_elems$' was declared here 87 | Seq<3> s("ACG"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_2_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:152:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_2_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:151:13: note: 's$_M_elems$' was declared here 151 | Seq<16> s("TTTTTTTTTTTTTTTT"); | ^ In member function 'Seq Seq::operator<<(char) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'virtual void Seq_Test16_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:147:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:266:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 266 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/seq_test.cpp:146:13: note: 's$_M_elems$' was declared here 146 | Seq<16> s("AAAAAAAAAAAAAAAA"); | ^ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/rtseq.hpp:20, from /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:8: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 5; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 5; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:337:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:329:12: note: 's$_M_elems$' was declared here 329 | Seq<5> s("CGTAC"); | ^ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 10; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 10; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:338:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:330:13: note: 's1$_M_elems$' was declared here 330 | Seq<10> s1("ACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 16; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 16; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:339:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:331:13: note: 's2$_M_elems$' was declared here 331 | Seq<16> s2("CCCCGTACGTACGTAC"); | ^~ In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 32; T = long unsigned int]', inlined from 'std::string Seq::str() const [with long unsigned int size_ = 32; T = long unsigned int]' at /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:385:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:340:5: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/sequence/seq.hpp:228:39: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 228 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/rtseq_test.cpp:332:13: note: 's3$_M_elems$' was declared here 332 | Seq<32> s3("ACGTACGTACACGTACGTACACGTACGTACAC"); | ^~ [100%] Linking CXX executable ../../bin/include_test cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/cmake -E cmake_link_script CMakeFiles/include_test.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/include_test.dir/link.d CMakeFiles/include_test.dir/seq_test.cpp.o CMakeFiles/include_test.dir/sequence_test.cpp.o CMakeFiles/include_test.dir/rtseq_test.cpp.o CMakeFiles/include_test.dir/quality_test.cpp.o CMakeFiles/include_test.dir/nucl_test.cpp.o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o CMakeFiles/include_test.dir/binary_test.cpp.o CMakeFiles/include_test.dir/test.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/include_test ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/teamcity_gtest/libteamcity_gtest.a -lgtest ../../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[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target include_test make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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 -j12 test ARGS\+=--verbose ARGS\+=-j12 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 -j12 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 Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: include_test 1: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/include_test 1: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test 1: Test timeout computed to be: 10000000 test 2 Start 2: debruijn_test 2: Test command: /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/bin/debruijn_test 2: Working Directory: /build/reproducible-path/spades-4.0.0+dfsg1/src/.. 2: Test timeout computed to be: 10000000 1: Running main() from gtest_main.cpp 1: [==========] Running 58 tests from 7 test suites. 1: [----------] Global test environment set-up. 1: [----------] 20 tests from Seq 1: [ RUN ] Seq.Selector 1: [ OK ] Seq.Selector (0 ms) 1: [ RUN ] Seq.ShiftLeft 1: [ OK ] Seq.ShiftLeft (0 ms) 1: [ RUN ] Seq.ShiftRight 1: [ OK ] Seq.ShiftRight (0 ms) 1: [ RUN ] Seq.Str 1: [ OK ] Seq.Str (0 ms) 1: [ RUN ] Seq.HeadAndTail 1: [ OK ] Seq.HeadAndTail (0 ms) 1: [ RUN ] Seq.FromBiggerSeq 1: [ OK ] Seq.FromBiggerSeq (0 ms) 1: [ RUN ] Seq.FromType 1: [ OK ] Seq.FromType (0 ms) 1: [ RUN ] Seq.PushBack 1: [ OK ] Seq.PushBack (0 ms) 1: [ RUN ] Seq.Null 1: [ OK ] Seq.Null (0 ms) 1: [ RUN ] Seq.EndNull 1: [ OK ] Seq.EndNull (0 ms) 1: [ RUN ] Seq.StartNull 1: [ OK ] Seq.StartNull (0 ms) 1: [ RUN ] Seq.AddSymbolForNullValue 1: [ OK ] Seq.AddSymbolForNullValue (0 ms) 1: [ RUN ] Seq.End 1: [ OK ] Seq.End (0 ms) 1: [ RUN ] Seq.Start 1: [ OK ] Seq.Start (0 ms) 1: [ RUN ] Seq.Complex 1: [ OK ] Seq.Complex (0 ms) 1: [ RUN ] Seq.FromCharArray 1: [ OK ] Seq.FromCharArray (0 ms) 1: [ RUN ] Seq.ReverseComplement 1: [ OK ] Seq.ReverseComplement (0 ms) 1: [ RUN ] Seq.Test16 1: [ OK ] Seq.Test16 (0 ms) 1: [ RUN ] Seq.Test16_2 1: [ OK ] Seq.Test16_2 (0 ms) 1: [ RUN ] Seq.TestFirstLast 1: [ OK ] Seq.TestFirstLast (0 ms) 1: [----------] 20 tests from Seq (0 ms total) 1: 1: [----------] 6 tests from Sequence 1: [ RUN ] Sequence.Selector 1: [ OK ] Sequence.Selector (0 ms) 1: [ RUN ] Sequence.ZeroLength 1: [ OK ] Sequence.ZeroLength (0 ms) 1: [ RUN ] Sequence.NullValue 1: [ OK ] Sequence.NullValue (0 ms) 1: [ RUN ] Sequence.Sum 1: [ OK ] Sequence.Sum (0 ms) 1: [ RUN ] Sequence.Str 1: [ OK ] Sequence.Str (0 ms) 1: [ RUN ] Sequence.ReverseComplement 1: [ OK ] Sequence.ReverseComplement (0 ms) 1: [----------] 6 tests from Sequence (0 ms total) 1: 1: [----------] 23 tests from RtSeq 1: [ RUN ] RtSeq.Selector 1: [ OK ] RtSeq.Selector (0 ms) 1: [ RUN ] RtSeq.ShiftLeft 1: [ OK ] RtSeq.ShiftLeft (0 ms) 1: [ RUN ] RtSeq.ShiftLeftThis 1: [ OK ] RtSeq.ShiftLeftThis (0 ms) 1: [ RUN ] RtSeq.ShiftRight 1: [ OK ] RtSeq.ShiftRight (0 ms) 1: [ RUN ] RtSeq.ShiftRightThis 1: [ OK ] RtSeq.ShiftRightThis (0 ms) 1: [ RUN ] RtSeq.Str 1: [ OK ] RtSeq.Str (0 ms) 1: [ RUN ] RtSeq.HeadAndTail 1: [ OK ] RtSeq.HeadAndTail (0 ms) 1: [ RUN ] RtSeq.FromBiggerRtSeq 1: [ OK ] RtSeq.FromBiggerRtSeq (0 ms) 1: [ RUN ] RtSeq.FromSeq 1: [ OK ] RtSeq.FromSeq (0 ms) 1: [ RUN ] RtSeq.ToSeq 1: [ OK ] RtSeq.ToSeq (0 ms) 1: [ RUN ] RtSeq.FromType 1: [ OK ] RtSeq.FromType (0 ms) 1: [ RUN ] RtSeq.PushBack 1: [ OK ] RtSeq.PushBack (0 ms) 1: [ RUN ] RtSeq.PushBackThis 1: [ OK ] RtSeq.PushBackThis (0 ms) 1: [ RUN ] RtSeq.PushFront 1: [ OK ] RtSeq.PushFront (0 ms) 1: [ RUN ] RtSeq.PushFrontThis 1: [ OK ] RtSeq.PushFrontThis (0 ms) 1: [ RUN ] RtSeq.Null 1: [ OK ] RtSeq.Null (0 ms) 1: [ RUN ] RtSeq.AddSymbolForNullValue 1: [ OK ] RtSeq.AddSymbolForNullValue (0 ms) 1: [ RUN ] RtSeq.Complex 1: [ OK ] RtSeq.Complex (0 ms) 1: [ RUN ] RtSeq.FromCharArray 1: [ OK ] RtSeq.FromCharArray (0 ms) 1: [ RUN ] RtSeq.ReverseComplement 1: [ OK ] RtSeq.ReverseComplement (0 ms) 1: [ RUN ] RtSeq.16 1: [ OK ] RtSeq.16 (0 ms) 1: [ RUN ] RtSeq.16_2 1: [ OK ] RtSeq.16_2 (0 ms) 1: [ RUN ] RtSeq.FirstLast 1: [ OK ] RtSeq.FirstLast (0 ms) 1: [----------] 23 tests from RtSeq (0 ms total) 1: 1: [----------] 1 test from Quality 1: [ RUN ] Quality.Test 1: [ OK ] Quality.Test (0 ms) 1: [----------] 1 test from Quality (0 ms total) 1: 1: [----------] 1 test from Nucl 1: [ RUN ] Nucl.Test 1: [ OK ] Nucl.Test (0 ms) 1: [----------] 1 test from Nucl (0 ms total) 1: 1: [----------] 4 tests from CyclicHash 1: [ RUN ] CyclicHash.TestBasic 1: [ OK ] CyclicHash.TestBasic (0 ms) 1: [ RUN ] CyclicHash.TestBasicRtSeq 1: [ OK ] CyclicHash.TestBasicRtSeq (0 ms) 1: [ RUN ] CyclicHash.TestRC 1: [ OK ] CyclicHash.TestRC (0 ms) 1: [ RUN ] CyclicHash.TestRoll 1: [ OK ] CyclicHash.TestRoll (0 ms) 1: [----------] 4 tests from CyclicHash (0 ms total) 1: 1: [----------] 3 tests from Binary 1: [ RUN ] Binary.Simple 1: [ OK ] Binary.Simple (0 ms) 1: [ RUN ] Binary.Containers 1: [ OK ] Binary.Containers (0 ms) 1: [ RUN ] Binary.Variadic 1: [ OK ] Binary.Variadic (0 ms) 1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (0 ms total) 1: [ PASSED ] 58 tests. 1/2 Test #1: include_test ..................... Passed 0.00 sec 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 / 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: 0:00:00.000 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: 0:00:00.000 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: 0:00:00.000 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: 0:00:00.000 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: 0:00:00.000 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 (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic 2: [ OK ] Histogram.StrongWeakPtrBasic (0 ms) 2: [----------] 1 test from Histogram (0 ms total) 2: 2: [----------] 13 tests from PairedInfo 2: [ RUN ] PairedInfo.Construct 2: [ OK ] PairedInfo.Construct (0 ms) 2: [ RUN ] PairedInfo.Access 2: [ OK ] PairedInfo.Access (0 ms) 2: [ RUN ] PairedInfo.HalfAccess 2: [ OK ] PairedInfo.HalfAccess (0 ms) 2: [ RUN ] PairedInfo.Remove 2: [ OK ] PairedInfo.Remove (0 ms) 2: [ RUN ] PairedInfo.UnexistingEdges 2: [ OK ] PairedInfo.UnexistingEdges (0 ms) 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours 2: [ OK ] PairedInfo.Neighbours (0 ms) 2: [ RUN ] PairedInfo.DoubledInfo 2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours 2: [ OK ] PairedInfo.HalfNeighbours (0 ms) 2: [ RUN ] PairedInfo.MoreNeighbours 2: [ OK ] PairedInfo.MoreNeighbours (0 ms) 2: [ RUN ] PairedInfo.Merge 2: [ OK ] PairedInfo.Merge (0 ms) 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry 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 ] PairedInfo.RandomSymmetry (35 ms) 2: [----------] 13 tests from PairedInfo (35 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Trivial (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch (0 ms) 2: [ RUN ] OverlapAnalysis.Mismatch2 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Mismatch2 (0 ms) 2: [ RUN ] OverlapAnalysis.Deletion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Deletion (0 ms) 2: [ RUN ] OverlapAnalysis.Insertion 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Insertion (0 ms) 2: [ RUN ] OverlapAnalysis.QueryLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.QueryLonger (0 ms) 2: [ RUN ] OverlapAnalysis.RefLonger 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.RefLonger (0 ms) 2: [ RUN ] OverlapAnalysis.TrivialBoundedFlank 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.TrivialBoundedFlank (0 ms) 2: [ RUN ] OverlapAnalysis.PartialPerfectAlignment 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.PartialPerfectAlignment (0 ms) 2: [ RUN ] OverlapAnalysis.Unalignable 2: When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information. 2: [ OK ] OverlapAnalysis.Unalignable (0 ms) 2: [ RUN ] OverlapAnalysis.Large 2: [ OK ] OverlapAnalysis.Large (0 ms) 2: [ RUN ] OverlapAnalysis.SimpleGap 2: [ OK ] OverlapAnalysis.SimpleGap (0 ms) 2: [ RUN ] OverlapAnalysis.UndefinedBehavior 2: [ OK ] OverlapAnalysis.UndefinedBehavior (0 ms) 2: [----------] 13 tests from OverlapAnalysis (0 ms total) 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest 2: 0:00:00.036 1M / 11M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.036 1M / 11M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.037 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: 0:00:00.037 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.038 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (1 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.038 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.038 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.038 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: 0:00:00.038 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.039 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.039 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.039 1M / 13M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.039 1M / 13M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.039 1M / 13M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.039 1M / 13M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.039 1M / 13M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.039 1M / 13M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.040 1M / 13M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.040 1M / 13M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.040 1M / 13M 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: 0:00:00.040 1M / 13M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.051 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (55 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.095 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.095 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.095 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: 0:00:00.096 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: 0:00:00.107 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (53 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.148 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.149 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.149 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: 0:00:00.149 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: 0:00:00.160 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (53 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.202 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.202 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.202 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: 0:00:00.202 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: 0:00:00.214 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.214 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: 0:00:00.221 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (62 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.264 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.265 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.265 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: 0:00:00.265 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.273 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.273 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (65 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.330 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.330 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.330 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: 0:00:00.330 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.330 1M / 51M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.331 1M / 51M INFO General (simplification_test.cpp : 277) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.331 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.331 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.331 1M / 51M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.331 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: 0:00:00.331 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.342 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.343 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.368 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.423 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: 0:00:00.423 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.450 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.450 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (198 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.529 1M / 55M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.530 1M / 55M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.530 1M / 55M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.530 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: 0:00:00.530 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: 0:00:00.589 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:00.589 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) 2: 0:00:00.607 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.631 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: 0:00:00.631 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.657 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.657 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 (204 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:00.734 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.734 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.734 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.734 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: 0:00:00.734 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: 0:00:00.736 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.736 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) 2: 0:00:00.739 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.762 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: 0:00:00.762 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.772 2M / 159M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.772 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.772 2M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (100 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:00.835 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.835 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.835 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.835 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: 0:00:00.835 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.845 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.845 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.870 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.924 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: 0:00:00.924 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.950 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.950 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.950 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (191 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:01.026 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.026 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.026 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.026 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: 0:00:01.026 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:01.027 3M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.027 3M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) 2: 0:00:01.027 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.028 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: 0:00:01.028 3M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.029 3M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.029 3M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.029 3M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (9 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:01.036 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.036 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.036 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.036 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.036 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.036 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.036 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) 2: 0:00:01.036 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.036 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: 0:00:01.036 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.037 1M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.037 1M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.037 1M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (4 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:01.040 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.040 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.040 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.040 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: 0:00:01.040 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:01.040 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.040 4M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) 2: 0:00:01.041 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.044 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: 0:00:01.044 4M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.046 4M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.046 4M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.046 4M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (16 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:01.056 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.056 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.056 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.057 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:01.057 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:01.057 2M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:01.057 2M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) 2: 0:00:01.057 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.057 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: 0:00:01.057 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.057 2M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:01.057 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 (1022 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:01.058 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.059 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.059 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.059 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.059 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.059 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.059 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.062 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 2 reads 2: 0:00:01.062 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.064 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.064 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.064 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.064 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.064 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.064 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.067 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. 2: 0:00:01.067 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.071 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. 2: 0:00:01.071 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.072 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: 0:00:01.072 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.072 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.073 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.073 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.073 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.073 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.073 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.073 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.073 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.073 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.073 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (20 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:01.079 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.079 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.079 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.079 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.079 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.079 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.079 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.084 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.084 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.085 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. 2: 0:00:01.086 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.086 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.086 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.086 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.086 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.089 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. 2: 0:00:01.089 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.091 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. 2: 0:00:01.091 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.092 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: 0:00:01.092 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.095 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.096 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.096 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.096 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.096 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.096 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.096 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.096 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.096 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.096 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (21 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:01.101 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.103 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.103 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.104 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.104 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.104 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.104 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.108 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.108 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.112 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.112 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.112 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.112 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.112 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.112 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.117 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:01.118 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.119 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.119 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.120 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: 0:00:01.120 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.136 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.136 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.136 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.136 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.136 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.137 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.137 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.137 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.137 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:01.137 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (64 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:01.165 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.166 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.166 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.166 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.166 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.166 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.166 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.170 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.170 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.172 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.172 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.172 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.173 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.173 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.173 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.176 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:01.177 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.179 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:01.179 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.180 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: 0:00:01.180 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.186 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.186 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.186 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.186 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.186 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:01.186 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.186 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.186 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.186 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.186 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create 2: 0:00:01.186 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.186 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.186 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.187 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.187 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.187 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:01.187 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (24 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:01.190 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.190 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.190 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.190 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.190 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.190 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.190 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.195 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.195 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.200 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.200 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.200 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.200 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.200 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.200 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.205 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. 2: 0:00:01.205 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.208 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:01.208 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.209 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: 0:00:01.209 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.214 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.215 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.215 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.215 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.215 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:01.215 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.215 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.215 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.215 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.215 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (26 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:01.216 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.216 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.216 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.216 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.216 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.216 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.216 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.221 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.222 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.223 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.224 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.224 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.224 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.224 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.224 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.227 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.228 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.235 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.235 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.236 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: 0:00:01.236 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.239 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.239 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.239 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.239 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.239 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.239 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.239 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.239 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.239 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.239 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (29 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:01.245 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.245 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.245 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.245 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.245 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.245 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.246 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.246 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.250 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.250 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.252 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.252 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.252 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.252 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.252 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.252 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.255 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.256 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.257 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.257 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.258 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: 0:00:01.258 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.259 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.259 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.259 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.259 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.259 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.259 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.260 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.260 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.260 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.260 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.282 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.282 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.282 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.282 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: 0:00:01.282 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (37 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:01.282 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.282 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.282 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.283 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.283 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.283 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.283 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.283 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.287 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.287 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.355 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.355 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.355 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.355 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.355 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.355 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.360 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.361 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.365 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.365 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.368 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: 0:00:01.368 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.369 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.369 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.369 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.369 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.369 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.369 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.369 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.369 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.369 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.369 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.374 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.374 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.374 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.374 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: 0:00:01.374 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (92 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:01.375 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.375 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.375 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.375 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 2: 0:00:01.375 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.375 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.375 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.375 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.380 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.380 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.381 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. 2: 0:00:01.381 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.381 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.381 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.381 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.381 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.384 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. 2: 0:00:01.385 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.389 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.390 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.390 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: 0:00:01.390 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.391 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.391 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.391 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.391 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.391 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:01.391 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.391 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.392 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.392 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create 2: 0:00:01.392 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.392 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.392 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) 2: 0:00:01.392 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.392 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: 0:00:01.392 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.392 1M / 159M INFO General (graph_construction.hpp : 94) Filling coverage index 2: 0:00:01.392 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.393 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: 0:00:01.393 1M / 159M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:01.393 1M / 159M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM 2: 0:00:01.393 1M / 159M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:01.393 1M / 159M INFO General (graph_pack_helpers.cpp : 56) Normalizing done 2: 0:00:01.396 14M / 159M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping 2: 0:00:01.397 14M / 159M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (25 ms) 2: [----------] 9 tests from GraphConstruction (341 ms total) 2: 2: [----------] 4 tests from Io 2: [ RUN ] Io.Order 2: 0:00:01.400 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.400 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.445 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.445 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (45 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (5 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [ RUN ] Io.GFADBG 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.452 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.452 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.452 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.452 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.452 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: 0:00:01.452 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started 2: 0:00:01.453 49M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp 2: 0:00:01.457 49M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.457 49M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.GFADBG (9 ms) 2: [----------] 4 tests from Io (60 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:01.461 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.461 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.461 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: 0:00:01.461 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.463 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (2 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove 2: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.464 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: 0:00:01.464 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.464 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: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.464 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: 0:00:01.464 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.464 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: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.464 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.464 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: 0:00:01.464 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.464 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: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.465 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: 0:00:01.465 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.465 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: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.465 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: 0:00:01.465 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.465 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: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.465 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.465 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: 0:00:01.465 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.466 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: 0:00:01.466 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.466 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.466 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: 0:00:01.466 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.466 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 (5 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:01.466 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.466 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.466 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: 0:00:01.466 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.466 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: 0:00:01.467 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.467 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.467 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: 0:00:01.467 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.467 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: 0:00:01.467 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.467 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.467 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: 0:00:01.467 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.467 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:01.467 1M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:01.467 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.468 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.468 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: 0:00:01.468 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.474 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.474 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:01.475 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.475 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.475 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: 0:00:01.475 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.481 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.481 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:01.482 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.482 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.482 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: 0:00:01.482 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.488 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.488 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.488 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:01.489 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.489 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.489 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: 0:00:01.489 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.495 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.495 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:01.496 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.496 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.496 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: 0:00:01.496 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.502 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.502 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.502 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:01.503 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.503 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.503 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: 0:00:01.503 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.509 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.509 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.509 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:01.510 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.510 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.510 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: 0:00:01.510 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.516 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.516 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.516 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (6 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:01.517 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.517 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.517 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: 0:00:01.517 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.523 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.523 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.524 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (7 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:01.524 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.524 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.524 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: 0:00:01.524 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.530 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (6 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:01.531 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.531 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.531 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: 0:00:01.531 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.537 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (6 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:01.538 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.538 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.538 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: 0:00:01.538 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.544 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:01.545 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.545 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.545 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: 0:00:01.545 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.552 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:01.552 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.552 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.552 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: 0:00:01.552 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.559 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:01.559 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.559 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.559 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: 0:00:01.559 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.566 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (6 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:01.566 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.566 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.566 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: 0:00:01.566 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.573 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.573 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.573 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (6 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:01.573 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.573 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.573 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: 0:00:01.573 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.580 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.580 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.580 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (6 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:01.580 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.580 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.580 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: 0:00:01.580 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.587 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.587 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.587 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (6 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:01.587 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.587 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.587 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: 0:00:01.587 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.594 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.594 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.594 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (6 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:01.594 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.594 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.594 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: 0:00:01.594 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.601 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.601 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.601 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (7 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:01.601 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.601 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.601 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: 0:00:01.601 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.608 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.608 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.608 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (6 ms) 2: [----------] 23 tests from OverlapRemoval (141 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:01.608 1M / 159M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:01.608 1M / 159M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 2: 0:00:01.608 1M / 159M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:01.608 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.608 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.608 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: 0:00:01.608 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.615 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.615 4M / 159M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' 2: 0:00:01.621 5M / 159M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (520 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:02.129 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.129 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.129 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: 0:00:02.129 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.135 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (7 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:02.136 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.136 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.136 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: 0:00:02.136 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.142 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (7 ms) 2: [----------] 5 tests from GraphAligner (534 ms total) 2: 2: [----------] 1 test from VariableOverlaps 2: [ RUN ] VariableOverlaps.BasicOperations 2: 0:00:02.143 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.143 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:02.143 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.143 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. (2143 ms total) 2: [ PASSED ] 100 tests. 2/2 Test #2: debruijn_test .................... Passed 2.15 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 2.16 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 -j12 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 make[2]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-bwa -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-corrector-core -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/corrector/corrector.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/hammer/config.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-ionhammer -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/ionhammer -- 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/pe_params.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/sewage_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/metaplasmid_mode.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/rna_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/hmm_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/metaviral_mode.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/config.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/detail_info_printer.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/careful_mda_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/meta_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/biosynthetic_spades_hmms -- 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/CStart.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/AMP.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/biosynthetic_spades_hmms/AT.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/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 -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/plasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaviralspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/metaplasmidspades.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/rnaviralspades.py -- 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/commands_parser.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/preprocess_interlaced_reads.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/correction_iteration_script.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/copy_files.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/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/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/process_cfg.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/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/check_test_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/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/terminating_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/breaking_scaffolds_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/scaffold_correction_stage.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/spades_iteration_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/alignment.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/__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/options_storage.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/test_dataset -- 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/genes_1K.txt -- 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.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/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_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/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 -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gsimplifier -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmercount -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-read-filter -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-kmer-estimating -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gfa-split -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/LICENSE -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/GPLv2.txt make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' # Use Debian-packaged yaml module find debian/spades \ -type f \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + mkdir -p debian/spades/usr/libexec/spades/ mv debian/spades/usr/bin/* debian/spades/usr/libexec/spades/ rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md rm -f debian/spades/usr/share/spades/GPLv2.txt rm -f debian/spades/usr/share/spades/README.md rm -f debian/spades/usr/share/spades/LICENSE make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_install -O--sourcedirectory=src -O--buildsystem=cmake dh_installdocs -O--sourcedirectory=src -O--buildsystem=cmake dh_installchangelogs -O--sourcedirectory=src -O--buildsystem=cmake dh_installexamples -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1' mkdir -p /build/reproducible-path/spades-4.0.0+dfsg1/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.adoc cp /build/reproducible-path/spades-4.0.0+dfsg1/debian/man_src/*.? /build/reproducible-path/spades-4.0.0+dfsg1/debian/man dh_installman make[1]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1' dh_python3 -O--sourcedirectory=src -O--buildsystem=cmake dh_installsystemduser -O--sourcedirectory=src -O--buildsystem=cmake dh_lintian -O--sourcedirectory=src -O--buildsystem=cmake dh_perl -O--sourcedirectory=src -O--buildsystem=cmake dh_link -O--sourcedirectory=src -O--buildsystem=cmake dh_strip_nondeterminism -O--sourcedirectory=src -O--buildsystem=cmake dh_compress -O--sourcedirectory=src -O--buildsystem=cmake dh_fixperms -O--sourcedirectory=src -O--buildsystem=cmake dh_missing -O--sourcedirectory=src -O--buildsystem=cmake dh_dwz -a -O--sourcedirectory=src -O--buildsystem=cmake dh_strip -a -O--sourcedirectory=src -O--buildsystem=cmake dh_makeshlibs -a -O--sourcedirectory=src -O--buildsystem=cmake dh_shlibdeps -a -O--sourcedirectory=src -O--buildsystem=cmake dh_installdeb -O--sourcedirectory=src -O--buildsystem=cmake 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+dfsg1-2_amd64.deb'. dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_4.0.0+dfsg1-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_4.0.0+dfsg1-2_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_4.0.0+dfsg1-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3074602/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3074602/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/3074602 and its subdirectories I: Current time: Mon Mar 23 21:23:20 +14 2026 I: pbuilder-time-stamp: 1774250600