I: pbuilder: network access will be disabled during build I: Current time: Mon Feb 17 12:36:44 -12 2025 I: pbuilder-time-stamp: 1739839004 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/2995195/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4279e146b62e47138a6de602182799e9' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2995195' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ojK6xN1t/pbuilderrc_6w8C --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ojK6xN1t/b1 --logfile b1/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+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2995195/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 7s (32.5 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) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20182 files and directories currently installed.) 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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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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/spades-4.0.0+dfsg1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_4.0.0+dfsg1-2_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 (24.1s) -- 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[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[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/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/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/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/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/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 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/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/CMakeFiles/easel.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/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]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build.make _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/build make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[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/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build [ 0%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32_fold.c.o make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/lexy/src/CMakeFiles/lexy_file.dir/build.make ext/lexy/src/CMakeFiles/lexy_file.dir/build 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 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-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 make[4]: Entering 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 [ 0%] 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 [ 0%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o 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 [ 0%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/adler32.c.o make[4]: Entering 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 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 make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 1%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.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/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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compare256.c.o [ 2%] Building CXX object ext/lexy/src/CMakeFiles/lexy_file.dir/input/file.cpp.o [ 2%] 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/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/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/_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 [ 2%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 2%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 2%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o 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/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 [ 2%] Building C object ext/easel/CMakeFiles/easel.dir/easel.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/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 2%] 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 [ 2%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/compress.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -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 [ 2%] 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 [ 3%] 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 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 [ 3%] 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 [ 3%] 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 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' [ 3%] 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 [ 3%] Built target lexy_file [ 3%] 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 [ 3%] 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 [ 3%] 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 [ 3%] 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 [ 3%] 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 [ 4%] 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 [ 4%] 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 [ 6%] 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 [ 6%] 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 [ 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 [ 6%] 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 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 make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend [ 6%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/deflate_rle.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 && /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=" 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 7%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/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 [ 7%] 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 [ 7%] 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 /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' [ 7%] Built target gqf [ 7%] 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 make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend [ 8%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/functable.c.o [ 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 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 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=" [ 8%] 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 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]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 9%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.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 [ 9%] 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 [ 9%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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 [ 9%] 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 [ 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 [ 9%] 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 [ 9%] 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 [ 9%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/genomic_info.cpp 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 [ 9%] 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 [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o [ 10%] 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_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 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 /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' [ 10%] Built target edlib make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 12%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/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 make -f common/kmer_index/CMakeFiles/mph_index.dir/build.make common/kmer_index/CMakeFiles/mph_index.dir/depend [ 12%] 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 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=" 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 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' [ 12%] 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 [ 12%] 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 /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' [ 12%] 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 /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_ ? | ^~~~~~~ [ 12%] Built target version 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=" 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' [ 13%] 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 [ 13%] 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 [ 13%] 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/slide_hash.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/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 [ 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 /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' [ 14%] 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 [ 14%] Built target teamcity_gtest [ 14%] 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 [ 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/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 [ 14%] 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 [ 14%] 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 [ 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 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 [ 14%] 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 [ 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 [ 15%] Linking CXX static library libformat.a 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 /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' 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 [ 15%] 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 [ 15%] Built target mph_index [ 17%] 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 [ 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/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 /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' [ 17%] Built target format [ 17%] 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 [ 17%] 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 [ 17%] 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 [ 17%] 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 /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); | ^~~~~~ [ 17%] 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 [ 17%] 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 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); | ^~~~~~ [ 18%] 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 [ 18%] 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 [ 18%] 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 [ 18%] 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 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 [ 18%] 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 [ 18%] 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 /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' [ 18%] 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 [ 18%] Built target sequence [ 19%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -msse4.2 -fno-lto -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/insert_string_sse42.c [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_iset.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_iset.c.o -MF CMakeFiles/easel.dir/esl_iset.c.o.d -o CMakeFiles/easel.dir/esl_iset.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_iset.c [ 19%] 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 [ 20%] 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 [ 20%] 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 [ 20%] 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 [ 20%] 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 [ 20%] 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 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 20%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -MF CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o.d -o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/arch/x86/chunkset_sse2.c [ 20%] 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 [ 20%] 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 [ 21%] 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 [ 21%] 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 [ 21%] 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 [ 21%] 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 [ 21%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msa.c [ 21%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o [ 21%] 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/_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 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 [ 21%] 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 [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile2.c [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_msafile_a2m.c [ 23%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 23%] Built target mimalloc-obj make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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' [ 23%] 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 [ 24%] 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 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-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 [ 24%] 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 [ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzlib.c.o [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_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 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 [ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzread.c.o [ 24%] 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/_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 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 [ 24%] 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 /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' [ 24%] Built target coverage_model [ 24%] Building C object _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build && /usr/bin/cc -DHAVE_ALIGNED_ALLOC -DHAVE_ATTRIBUTE_ALIGNED -DHAVE_BUILTIN_CTZ -DHAVE_BUILTIN_CTZLL -DHAVE_POSIX_MEMALIGN -DHAVE_SYS_AUXV_H -DHAVE_THREAD_LOCAL -DHAVE_VISIBILITY_HIDDEN -DHAVE_VISIBILITY_INTERNAL -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -DWITH_GZFILEOP -DX86_AVX2 -DX86_AVX512 -DX86_AVX512VNNI -DX86_FEATURES -DX86_MASK_INTRIN -DX86_PCLMULQDQ_CRC -DX86_SSE2 -DX86_SSE42 -DX86_SSSE3 -DX86_VPCLMULQDQ_CRC -DZLIB_COMPAT -D_LARGEFILE64_SOURCE=1 -D__USE_LARGEFILE64 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c11 -Wno-deprecated -O2 -Wall -MD -MT _deps/zlib_ng-build/CMakeFiles/zlibstatic.dir/gzwrite.c.o -MF CMakeFiles/zlibstatic.dir/gzwrite.c.o.d -o CMakeFiles/zlibstatic.dir/gzwrite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng/gzwrite.c [ 24%] 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 [ 24%] 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 [ 25%] 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 [ 25%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/utils/filesystem/temporary.cpp [ 25%] 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 [ 25%] 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 [ 26%] 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 [ 26%] 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 [ 26%] 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_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o 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CMakeFiles/zlibstatic.dir/deflate_stored.c.o CMakeFiles/zlibstatic.dir/functable.c.o CMakeFiles/zlibstatic.dir/infback.c.o CMakeFiles/zlibstatic.dir/inflate.c.o CMakeFiles/zlibstatic.dir/inftrees.c.o CMakeFiles/zlibstatic.dir/insert_string.c.o CMakeFiles/zlibstatic.dir/insert_string_roll.c.o CMakeFiles/zlibstatic.dir/slide_hash.c.o CMakeFiles/zlibstatic.dir/trees.c.o CMakeFiles/zlibstatic.dir/uncompr.c.o CMakeFiles/zlibstatic.dir/zutil.c.o CMakeFiles/zlibstatic.dir/arch/x86/x86_features.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_avx512_vnni.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/insert_string_sse42.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/compare256_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/slide_hash_sse2.c.o CMakeFiles/zlibstatic.dir/arch/x86/adler32_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/chunkset_ssse3.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_pclmulqdq.c.o CMakeFiles/zlibstatic.dir/arch/x86/crc32_vpclmulqdq.c.o CMakeFiles/zlibstatic.dir/gzlib.c.o CMakeFiles/zlibstatic.dir/gzread.c.o CMakeFiles/zlibstatic.dir/gzwrite.c.o /usr/bin/ranlib libz.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 26%] Built target zlibstatic make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend [ 26%] 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 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' [ 28%] 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 [ 28%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_normal.c [ 28%] 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 [ 29%] 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 [ 29%] 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 [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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29%] 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 [ 29%] 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 [ 29%] 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 [ 29%] 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 [ 29%] 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 [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o [ 30%] 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/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 [ 30%] 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/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/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 [ 31%] 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 [ 31%] 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 [ 32%] 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 [ 32%] 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 [ 32%] 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 [ 32%] 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o [ 34%] 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 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 [ 34%] 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 [ 34%] 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 [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o [ 34%] 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/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 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 [ 34%] 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 [ 34%] 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 [ 34%] 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] 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 [ 34%] 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 [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_scorematrix.c [ 35%] 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 [ 35%] 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 [ 35%] 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 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__ | ^~~~~~ [ 35%] 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 [ 35%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Hashing.cpp [ 35%] 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 [ 35%] 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 [ 35%] 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 [ 35%] 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 [ 35%] 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 [ 36%] 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 [ 37%] 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 [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.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/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/LEB128.cpp 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); | ^~~~~~~~ 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=" [ 37%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f 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-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 [ 37%] 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%] 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 [ 37%] 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 [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o [ 37%] Linking C static library libsamtools.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/MD5.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 [ 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/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 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 [ 37%] 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 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o CMakeFiles/utils.dir/logger/log_writers.cpp.o CMakeFiles/utils.dir/logger/log_writers_thread.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 39%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o [ 40%] 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/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 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 [ 40%] 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 [ 40%] Built target utils 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' /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 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' [ 41%] 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 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' [ 41%] 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 [ 41%] Built target samtools make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 41%] 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 [ 41%] 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 [ 41%] 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 [ 41%] 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/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 [ 41%] 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 [ 41%] 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 [ 41%] 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 /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 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /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() | | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/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 [ 41%] 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 /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]}; | ^~~ 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; | ^~~~~~~~ [ 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 42%] 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 [ 43%] 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 [ 43%] 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 [ 43%] 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 [ 43%] 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 [ 43%] 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 [ 45%] 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 [ 45%] 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 [ 45%] 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 [ 45%] 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 [ 45%] 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 [ 45%] 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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building C object ext/bwa/CMakeFiles/bwa.dir/rle.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/bwa.dir/rle.c.o -MF CMakeFiles/bwa.dir/rle.c.o.d -o CMakeFiles/bwa.dir/rle.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/rle.c [ 45%] Building 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 [ 45%] 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 [ 45%] 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 [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o [ 45%] Linking CXX static library libsamio.a 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 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/common/io/sam && /usr/bin/cmake -E cmake_link_script CMakeFiles/samio.dir/link.txt --verbose=1 [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/llvm/Twine.cpp [ 46%] 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 [ 47%] 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 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 [ 47%] 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 [ 48%] 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 [ 48%] 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 /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' [ 48%] Built target bwa make -f ext/bwa/CMakeFiles/spades-bwa.dir/build.make ext/bwa/CMakeFiles/spades-bwa.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa/CMakeFiles/spades-bwa.dir/DependInfo.cmake "--color=" [ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-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 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' [ 48%] 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 [ 48%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/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/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 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( | ^~~~~~~~~~ [ 48%] 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 /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' [ 48%] 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/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 [ 48%] Built target samio [ 48%] 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 [ 48%] 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 [ 50%] 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 [ 50%] 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 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( | ^~~~~~~~~~ [ 50%] 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 [ 50%] 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 [ 50%] 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 [ 51%] 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 [ 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 [ 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 [ 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 [ 52%] 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 [ 52%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtaln.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-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 [ 52%] 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 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) | ^~~~~~ [ 52%] 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 [ 52%] 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/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/easel/CMakeFiles/easel.dir/esl_workqueue.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel/esl_workqueue.c [ 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 [ 53%] 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 [ 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 [ 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 [ 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 [ 53%] 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/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 [ 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 [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwashm.c.o [ 56%] 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 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 [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -MF CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o.d -o CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwtsw2_aux.c [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o 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 /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%] 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 [ 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/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 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 [ 56%] Building C object ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/bwa && /usr/bin/cc -DHAVE_PTHREAD -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bwa/CMakeFiles/spades-bwa.dir/bwt_lite.c.o -MF CMakeFiles/spades-bwa.dir/bwt_lite.c.o.d -o CMakeFiles/spades-bwa.dir/bwt_lite.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/bwa/bwt_lite.c [ 57%] Building C object ext/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 /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 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CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_red_black.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_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' [ 57%] 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 [ 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 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ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 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/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/cachedb.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/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 [ 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 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); | ^~~ [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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 [ 58%] Linking C executable ../../bin/spades-bwa [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o 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 [ 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 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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 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 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_banded.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/generic_fwdback_banded.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-bwa.dir/link.d "CMakeFiles/spades-bwa.dir/main.c.o" "CMakeFiles/spades-bwa.dir/fastmap.c.o" "CMakeFiles/spades-bwa.dir/pemerge.c.o" "CMakeFiles/spades-bwa.dir/maxk.c.o" "CMakeFiles/spades-bwa.dir/kopen.c.o" "CMakeFiles/spades-bwa.dir/bwtaln.c.o" "CMakeFiles/spades-bwa.dir/bwtgap.c.o" "CMakeFiles/spades-bwa.dir/bwaseqio.c.o" "CMakeFiles/spades-bwa.dir/bamlite.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o" "CMakeFiles/spades-bwa.dir/bwashm.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o" "CMakeFiles/spades-bwa.dir/bwt_lite.c.o" "CMakeFiles/spades-bwa.dir/bwape.c.o" "CMakeFiles/spades-bwa.dir/bwase.c.o" "CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o" -o ../../bin/spades-bwa libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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 [ 59%] 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 [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o [ 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_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 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 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/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 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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%] Linking CXX static library libllvm-support.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.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/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 [ 62%] Built target spades-bwa [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/hmmdwrkr.c [ 63%] 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 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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/logsum.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem 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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 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 [ 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/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/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%] 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 [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o [ 64%] 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 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-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 [ 64%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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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_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 [ 64%] 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 [ 64%] 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 [ 65%] 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 [ 65%] 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 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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 [ 65%] 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 && /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 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"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' [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o [ 65%] 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 -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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-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 [ 65%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-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_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmm.c [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.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 && /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/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_hmmcache.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-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_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 make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 67%] 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 [ 67%] Linking CXX static library libbinary_io.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o [ 67%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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 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_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_null3.c [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o cd 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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 [ 68%] 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 [ 69%] 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 [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.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_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 [ 69%] 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 [ 69%] 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 /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' [ 69%] Built target binary_io make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend [ 69%] 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 -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_tophits.c [ 69%] 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 [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.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 && /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=" 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_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 [ 69%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src/p7_scoredata.c make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hit.c.o [ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/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 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 [ 70%] 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 [ 70%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domain.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /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_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 [ 70%] 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 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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 [ 70%] 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 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common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 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-I/build/reproducible-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 [ 73%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o [ 73%] Linking CXX static library libgraphio.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 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF 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/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-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 [ 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 && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer 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/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 [ 74%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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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 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' [ 74%] 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 [ 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 [ 74%] 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 [ 74%] 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 [ 74%] 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 [ 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 CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o 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 | } | ^ 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 [ 75%] 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 [ 75%] 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 [ 75%] 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 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); | ^~~~~~ [ 75%] 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 /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], | ^~~~~~ [ 75%] 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 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_; | ^~~~~~~~ /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' [ 75%] 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' [ 75%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp [ 75%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp: In constructor 'hmmer::HMMFile::HMMFile(const std::string&)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:53:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 53 | p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:55:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 55 | p7_Fail("File format problem in trying to open HMM file %s.\n%s\n", hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmfile.cpp:57:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 57 | p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, hmmfile.c_str(), errbuf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/hmm/hmmmatcher.cpp:166:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 166 | pli->Z = pli->domZ = cfg.Z; | ~~~~^ [ 75%] 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' [ 75%] 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' [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o [ 75%] 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/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/gap_closer.cpp [ 75%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/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 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/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/second_phase_setup.cpp [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/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/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 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 [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/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()); | ^~~~ [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/hybrid_aligning.cpp [ 76%] Linking CXX static library libtoolchain.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -P CMakeFiles/toolchain.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/toolchain && /usr/bin/cmake -E cmake_link_script CMakeFiles/toolchain.dir/link.txt --verbose=1 /usr/bin/ar qc libtoolchain.a CMakeFiles/toolchain.dir/utils.cpp.o /usr/bin/ranlib libtoolchain.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 76%] Built target toolchain [ 76%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/easel -isystem /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/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 [ 78%] 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%] 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 [ 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; | ^~~~~~~ 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()); | ^~~ /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' [ 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 [ 79%] 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' [ 79%] 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 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], | ^~~~~~ /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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 79%] 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/io/binary/graph_pack.hpp:10, from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph/stats/picture_dump.hpp:18, from /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades/repeat_resolving.cpp:11: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:30:10: required from here 30 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:31:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 31 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:43:10: required from here 43 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:44:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 44 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/basic.hpp:10: /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:47:10: required from here 47 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:61:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 61 | auto new_id = graph.AddVertex(typename Graph::VertexData(graph.k()), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/binary/graph.hpp:83:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 83 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/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/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], | ^~~~~~ /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()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ [ 79%] 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 [ 79%] 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 [ 79%] 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 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 [ 80%] 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' [ 80%] 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=" 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' [ 80%] 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 [ 81%] 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 [ 81%] 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' [ 81%] Built target assembly_graph make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 81%] Building CXX object common/alignment/CMakeFiles/alignment.dir/gap_info.cpp.o [ 81%] 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/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 [ 81%] 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/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 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 [ 81%] 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 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 [ 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 /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) | ~~~~~~~~~~~~~~~~^~~~~ [ 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 [ 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 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 | } | ^ 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( | ^~~~~~~~~~ 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( | ^~~~~~~~~~ [ 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 [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o [ 82%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o [ 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/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/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules/path_extend/gap_analyzer.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+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 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 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 [ 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/launcher.cpp.o [ 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 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%] 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 /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]; | ^~~ /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' [ 84%] Built target alignment make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend [ 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 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' [ 84%] 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 [ 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 /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_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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], | ^~~~~~ 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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 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( | ^~~~~~~~~~ [ 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 [ 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 [ 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 /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_) { | ^~~~~~~~~~~~~~~ [ 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 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 [ 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 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/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/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/weighted_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/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/paired_info/weighted_distance_estimation.cpp [ 86%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/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 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/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 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/graph_pack_helpers.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack_helpers.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/pipeline/graph_pack_helpers.cpp [ 86%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/sequence_mapper_gp_api.cpp.o 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 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 /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], | ^~~~~~ 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 /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( | ^~~~~~~~~~ [ 87%] Linking CXX static library libpaired_info.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 [ 87%] Linking CXX static library libpipeline.a cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o CMakeFiles/paired_info.dir/paired_info_utils.cpp.o CMakeFiles/paired_info.dir/distance_estimation_utils.cpp.o /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 87%] Built target paired_info /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' [ 87%] 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' 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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: 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' 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/construction.cpp.o [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o [ 87%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o [ 87%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o [ 89%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o [ 90%] 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/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=16777216UL -DBLAZE_USE_CPP_THREADS -DBLAZE_USE_DEBUG_MODE=0 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-fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/ionhammer/err_helper_table.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+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 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-I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/src/projects/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 [ 90%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/common/stages/read_conversion.cpp 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 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/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 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/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 [ 90%] 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/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 [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/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 /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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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; | ~~~~~~~~~~^~ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=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 [ 91%] 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 [ 91%] 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 [ 91%] 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 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) { | ~~~~~~~^~~~ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DBLAZE_CACHE_SIZE=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 [ 92%] 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%] 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 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 -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/depend make -f projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/build.make projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/depend make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/depend make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/depend make -f projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/depend 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/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[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[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[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-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-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-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools/CMakeFiles/spades-gfa-split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: 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/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 92%] 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/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 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]: 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-convert-bin-to-fasta.dir/build.make projects/spades_tools/CMakeFiles/spades-convert-bin-to-fasta.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-read-filter.dir/build.make projects/spades_tools/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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]: 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-kmer-estimating.dir/build.make projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build.make projects/spades_tools/CMakeFiles/spades-gfa-split.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-gfa-split.dir/gfa_split.cpp.o [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-gsimplifier.dir/__/cds_subgraphs/profile_storage.cpp.o [ 93%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o [ 97%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o [ 93%] Building CXX object projects/spades_tools/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o [ 97%] 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/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 [ 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_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/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++ -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 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-gmapper.dir/build.make projects/spades_tools/CMakeFiles/spades-gmapper.dir/build 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 make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/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-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 make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f projects/spades_tools/CMakeFiles/spades-kmercount.dir/build.make projects/spades_tools/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/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 [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-gmapper.dir/gmapper.cpp.o [ 97%] Building CXX object projects/spades_tools/CMakeFiles/spades-kmercount.dir/kmercount.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 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/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 /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, | ~~~~~~~~~~~^ /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)) { | ~~~~~~~~~~~~~~^~ [ 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/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 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'; | ^~~~ 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()); | ^~~ 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], | ^~~~~~ [ 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%] 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 [ 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 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/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 [ 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/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 [ 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); | ^~~ 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) { | ~~~~^~~~~~~~~~~ [ 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%] Linking CXX executable ../../bin/spades-corrector-core cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-4.0.0+dfsg1/src/common/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()); | ^~~ /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/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 [ 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 /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' /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-kmer-estimating [ 98%] Built target spades-corrector-core [ 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 [ 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%] 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-gfa-split cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gfa-split.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/reproducible-path/spades-4.0.0+dfsg1/src/projects/hammer/read_corrector.cpp:73:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 73 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 98%] Built target spades-read-filter [ 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 /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 [100%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/projects/spades_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-kmercount.dir/link.d "CMakeFiles/spades-kmercount.dir/kmercount.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/kmer_index/libmph_index.a ../../common/modules/libmodules.a ../../common/configs/libconfigs.a ../../common/library/liblibrary.a ../../common/io/libinput.a ../../common/io/sam/libsamio.a ../../ext/samtools/libsamtools.a /usr/lib/x86_64-linux-gnu/libbamtools.so ../../common/io/binary/libbinary_io.a ../../common/alignment/libalignment.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a /usr/lib/gcc/x86_64-linux-gnu/14/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/bwa/libbwa.a ../../_deps/zlib_ng-build/libz.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [100%] Built target spades-kmercount /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); | ^~~~~~~~~~ /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); | ^ /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/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()); | ^~~ /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; | ^~~ 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/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()); | ^~~ /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); | ^ 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()); | ^~~ 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/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], | ^~~~~~ /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/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); | ^~~ [ 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/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/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 { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 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 -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/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/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 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/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=" [ 4%] Built target coverage_model [ 4%] Built target mimalloc-obj [ 7%] Built target version [ 9%] Built target teamcity_gtest [ 9%] Built target mph_index make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend [ 19%] Built target binary_io [ 30%] Built target zlibstatic 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 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common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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]: 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' [ 30%] Built target sequence [ 52%] Built target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: 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 -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build 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/samtools/CMakeFiles/samtools.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/bwa/CMakeFiles/bwa.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/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 61%] Built target samtools [ 66%] Built target utils [ 71%] Built target bwa make -f common/io/sam/CMakeFiles/samio.dir/build.make common/io/sam/CMakeFiles/samio.dir/depend make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/io/sam/CMakeFiles/samio.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" 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]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target input make -f common/alignment/CMakeFiles/alignment.dir/build.make common/alignment/CMakeFiles/alignment.dir/build 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=" 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' 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 [ 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' 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]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" [ 80%] Built target library make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-4.0.0+dfsg1/src /build/reproducible-path/spades-4.0.0+dfsg1/src/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/common/configs/CMakeFiles/configs.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/configs/CMakeFiles/configs.dir/build.make common/configs/CMakeFiles/configs.dir/build 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' [ 85%] Built target modules [ 85%] Built target configs make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend 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/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' 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[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu' 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 [ 90%] Built target paired_info 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' [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o cd /build/reproducible-path/spades-4.0.0+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 [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools 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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/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 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/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 [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/binary_test.cpp cd /build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/usr/include/bamtools -I/build/reproducible-path/spades-4.0.0+dfsg1/src/include -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-4.0.0+dfsg1/src -I/build/reproducible-path/spades-4.0.0+dfsg1/src/common -I/build/reproducible-path/spades-4.0.0+dfsg1/obj-x86_64-linux-gnu/_deps/zlib_ng-build -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/zlib-ng -I/build/reproducible-path/spades-4.0.0+dfsg1/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-4.0.0+dfsg1/src/../ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-4.0.0+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -fopenmp -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-4.0.0+dfsg1/src/test/include_test/quality_test.cpp 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 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 0.01 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 100 tests from 11 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty 2: 0:00:00.000 1M / 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 (25 ms) 2: [----------] 13 tests from PairedInfo (25 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: 0:00:00.028 1M / 11M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.028 1M / 11M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.029 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: 0:00:00.029 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.029 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (4 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.030 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.030 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.030 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: 0:00:00.030 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.031 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (0 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.031 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.031 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.031 1M / 12M INFO General (graph_simplification.hpp : 657) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.031 1M / 12M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.031 1M / 12M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.031 1M / 12M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.042 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (45 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.077 1M / 50M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.077 1M / 50M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.077 1M / 50M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.077 1M / 50M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.085 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (44 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.121 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.121 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.121 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: 0:00:00.121 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: 0:00:00.129 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (44 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.165 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.165 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.165 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: 0:00:00.165 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: 0:00:00.174 623M / 623M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.174 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: 0:00:00.180 623M / 623M INFO General (single_cell_simplification: 56) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (49 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.214 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.215 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.215 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: 0:00:00.215 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.223 606M / 606M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.223 606M / 606M INFO General (single_cell_simplification: 133) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (54 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.269 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.269 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.269 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: 0:00:00.269 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.269 1M / 51M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.270 1M / 51M INFO General (simplification_test.cpp : 277) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (0 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.270 1M / 51M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.270 1M / 51M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.270 1M / 51M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.270 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: 0:00:00.270 1M / 51M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.277 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.277 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.298 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.341 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: 0:00:00.341 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.362 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.362 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (158 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.428 1M / 55M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.429 1M / 55M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.429 1M / 55M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.429 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: 0:00:00.429 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: 0:00:00.474 1160M / 1160M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:00.474 1160M / 1160M INFO General (edge_index.hpp : 175) Using small index (max_id = 21667994) 2: 0:00:00.488 1160M / 1160M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.507 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: 0:00:00.507 1161M / 1161M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.528 1161M / 1161M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.529 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 (164 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:00.593 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.593 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.593 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.593 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: 0:00:00.593 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: 0:00:00.598 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.598 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 3036) 2: 0:00:00.601 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.619 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: 0:00:00.619 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.626 2M / 159M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.627 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.628 2M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (62 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:00.656 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.656 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.656 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.656 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: 0:00:00.656 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.664 1172M / 1172M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.664 1172M / 1172M INFO General (edge_index.hpp : 175) Using small index (max_id = 21626308) 2: 0:00:00.686 1172M / 1172M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.729 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: 0:00:00.729 1172M / 1172M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.751 1172M / 1172M INFO General (graphio.cpp : 189) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.751 1172M / 1172M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.751 1172M / 1172M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (159 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:00.815 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.815 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.815 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.815 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: 0:00:00.815 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:00.816 3M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:00.816 3M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 35260) 2: 0:00:00.816 3M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.817 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: 0:00:00.817 3M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.818 3M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:00.818 3M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:00.819 3M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (9 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:00.825 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.825 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.825 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.825 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.825 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.825 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.825 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 12354) 2: 0:00:00.825 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.825 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: 0:00:00.825 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.826 1M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:00.826 1M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.826 1M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (2 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:00.827 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.827 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.827 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.827 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: 0:00:00.827 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:00.827 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:00.827 4M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 36400) 2: 0:00:00.828 4M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.830 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: 0:00:00.831 4M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.832 4M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:00.832 4M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:00.832 4M / 159M INFO General (simplification_test.cpp : 309) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (14 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:00.842 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.842 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.842 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:00.842 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:00.842 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:00.842 2M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:00.842 2M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 5512) 2: 0:00:00.842 2M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.842 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: 0:00:00.842 2M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:00.843 2M / 159M INFO General (graphio.cpp : 184) No positions were saved 2: 0:00:00.843 2M / 159M INFO General (graphio.cpp : 155) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: [ OK ] Simplification.CompressorTest (1 ms) 2: [----------] 17 tests from Simplification (817 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:00.843 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.843 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.845 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:00.845 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.845 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.845 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.845 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.849 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 2 reads 2: 0:00:00.849 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.850 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:00.850 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:00.850 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.851 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.851 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.851 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.853 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 6 kmers. 2: 0:00:00.853 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.854 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 7 kmers in total. 2: 0:00:00.854 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.854 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: 0:00:00.854 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:00.854 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:00.855 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.855 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:00.855 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:00.855 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:00.855 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:00.855 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.855 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:00.855 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:00.855 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (12 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:00.856 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.856 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.856 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:00.856 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.856 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.856 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.856 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.859 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:00.859 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.860 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 8 kmers in total. 2: 0:00:00.860 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:00.860 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.860 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.860 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.860 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.862 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 8 kmers. 2: 0:00:00.862 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.863 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 9 kmers in total. 2: 0:00:00.863 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.864 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: 0:00:00.864 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:00.883 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:00.883 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.883 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:00.883 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:00.883 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:00.883 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:00.883 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.883 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:00.883 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 2 edges to create 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:00.883 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (28 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:00.885 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.885 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.885 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:00.885 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.885 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.885 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.885 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.887 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:00.887 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.888 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.888 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:00.888 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.888 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.888 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.888 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.890 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:00.890 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.891 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.891 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.891 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: 0:00:00.891 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:00.931 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:00.931 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.931 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:00.931 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:00.931 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:00.931 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:00.931 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.931 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:00.931 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:00.931 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (47 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:00.933 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.933 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.933 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:00.933 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.933 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.933 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.933 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.935 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:00.935 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.936 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.936 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:00.936 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.936 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.936 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.936 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.937 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 11 kmers. 2: 0:00:00.938 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.938 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.938 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.939 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: 0:00:00.939 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:00.982 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:00.982 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.982 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:00.982 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:00.982 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:00.982 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:00.982 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.982 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:00.982 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 8 edges to create 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 4 vertices to create 2: 0:00:00.982 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (53 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:00.986 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.986 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:00.986 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:00.986 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.986 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.986 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.986 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.988 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:00.988 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.989 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.989 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:00.989 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.989 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:00.989 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.989 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:00.991 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 12 kmers. 2: 0:00:00.991 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:00.992 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.992 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:00.992 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: 0:00:00.992 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.029 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.029 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.029 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.029 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.029 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:01.029 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.029 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.029 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.029 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 4 edges to create 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 2 vertices to create 2: 0:00:01.029 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (48 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:01.034 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.034 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.034 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.034 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.034 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.034 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.034 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.036 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.036 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.037 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.037 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.037 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.037 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.037 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.037 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.039 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.039 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.040 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.040 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.040 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: 0:00:01.040 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.077 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.077 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.077 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.077 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.077 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.077 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.078 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.078 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.078 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.078 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (47 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:01.081 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.081 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.081 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.081 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.081 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.081 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.081 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.081 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.083 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.083 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.084 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.084 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.084 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.084 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.084 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.084 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.086 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.086 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.087 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.087 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.087 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: 0:00:01.087 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.126 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.127 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.127 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.127 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.127 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.127 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.127 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.131 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.131 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.131 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.131 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: 0:00:01.131 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (50 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:01.131 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.131 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.131 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.131 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=5 2: 0:00:01.131 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.131 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.131 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.131 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.134 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 8 reads 2: 0:00:01.134 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.134 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.134 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.134 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.134 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.135 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.135 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.136 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 13 kmers. 2: 0:00:01.137 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.137 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 13 kmers in total. 2: 0:00:01.137 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.138 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: 0:00:01.138 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.175 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.175 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.175 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.175 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.175 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:01.175 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.175 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.175 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.175 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 6 edges to create 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 3 vertices to create 2: 0:00:01.175 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.177 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.177 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 9) 2: 0:00:01.177 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.177 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: 0:00:01.177 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (46 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:01.177 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.177 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.177 1M / 159M INFO General (edge_index.hpp : 132) Size of edge index entries: 12/8 2: 0:00:01.178 1M / 159M INFO General (graph_construction.hpp : 46) Constructing DeBruijn graph for k=3 2: 0:00:01.178 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.178 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.178 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.178 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.180 1M / 159M INFO General (kmer_splitters.hpp : 134) Used 4 reads 2: 0:00:01.180 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.180 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 5 kmers in total. 2: 0:00:01.181 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 453) Building kmer index 2: 0:00:01.181 1M / 159M INFO General (kmer_index_builder.hpp : 258) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.181 1M / 159M INFO General (file_limit.hpp : 43) Open file limit set to 1024 2: 0:00:01.181 1M / 159M INFO General (kmer_splitter.hpp : 94) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.181 1M / 159M INFO General (kmer_splitter.hpp : 102) Using cell size of 6710886 2: 0:00:01.182 601M / 601M INFO General (kmer_splitters.hpp : 202) Used 5 kmers. 2: 0:00:01.182 1M / 159M INFO General (kmer_index_builder.hpp : 264) Starting k-mer counting. 2: 0:00:01.183 1M / 159M INFO General (kmer_index_builder.hpp : 275) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.183 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.183 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: 0:00:01.183 1M / 159M INFO General (kmer_index_builder.hpp : 168) Merging final buckets. 2: 0:00:01.223 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 101) Building k-mer extensions from k+1-mers 2: 0:00:01.223 1M / 159M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 106) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.223 1M / 159M INFO General (graph_construction.hpp : 58) Condensing graph 2: 0:00:01.223 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 381) Extracting unbranching paths 2: 0:00:01.223 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 400) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:01.223 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 336) Collecting perfect loops 2: 0:00:01.223 1M / 159M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 369) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.223 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 586) Sorting edges... 2: 0:00:01.223 1M / 159M INFO DeBruijnGraphConstructor (debruijn_graph_constructor: 588) Edges sorted 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 516) Total 10 edges to create 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 519) Collecting link records 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 521) Ordering link records 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 524) Sorting done 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 537) Sorting LinkRecords... 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 540) LinkRecords sorted 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 542) Total 6 vertices to create 2: 0:00:01.223 1M / 159M INFO General (debruijn_graph_constructor: 545) Connecting the graph 2: 0:00:01.227 1M / 159M INFO General (graph_construction.hpp : 80) Building index with from graph 2: 0:00:01.227 1M / 159M INFO General (edge_index.hpp : 175) Using small index (max_id = 13) 2: 0:00:01.227 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.227 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: 0:00:01.227 1M / 159M INFO General (edge_index_builders.hpp : 253) Collecting edge information from graph, this takes a while. 2: 0:00:01.227 1M / 159M INFO General (graph_construction.hpp : 94) Filling coverage index 2: 0:00:01.227 1M / 159M INFO K-mer Index Building (kmer_index_builder.hpp : 410) Building perfect hash indices 2: 0:00:01.227 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: 0:00:01.227 1M / 159M INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:01.227 1M / 159M INFO General (graph_construction.hpp : 100) Filling coverage and flanking coverage from PHM 2: 0:00:01.228 1M / 159M INFO General (graph_pack_helpers.cpp : 54) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:01.228 1M / 159M INFO General (graph_pack_helpers.cpp : 56) Normalizing done 2: 0:00:01.230 14M / 159M INFO General (sequence_mapper_notifier.h: 64) Starting sequence mapping 2: 0:00:01.231 14M / 159M INFO General (sequence_mapper_notifier.h: 103) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (55 ms) 2: [----------] 9 tests from GraphConstruction (390 ms total) 2: 2: [----------] 4 tests from Io 2: [ RUN ] Io.Order 2: 0:00:01.233 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.233 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.261 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.261 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (27 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (2 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [ RUN ] Io.GFADBG 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 39) Trying to read conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.264 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.264 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: 0:00:01.264 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from src/test/debruijn/graph_fragments/topology_ec/self_comp started 2: 0:00:01.267 49M / 159M INFO General (graphio.cpp : 139) Reading coverage from src/test/debruijn/graph_fragments/topology_ec/self_comp 2: 0:00:01.269 49M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.269 49M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] Io.GFADBG (7 ms) 2: [----------] 4 tests from Io (37 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:01.271 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.271 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.271 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: 0:00:01.271 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.274 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: 0:00:01.274 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.274 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.274 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: 0:00:01.274 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.274 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: 0:00:01.274 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.274 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.274 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: 0:00:01.274 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.275 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.275 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: 0:00:01.275 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.276 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 (4 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:01.276 1M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.276 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.276 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: 0:00:01.276 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.280 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.280 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:01.280 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.280 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.280 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: 0:00:01.280 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.284 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.284 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:01.284 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.284 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.284 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: 0:00:01.284 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.288 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.288 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.288 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:01.288 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.288 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.288 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: 0:00:01.288 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.291 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.292 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:01.292 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.292 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.292 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: 0:00:01.292 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.295 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.295 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.295 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:01.295 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.296 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.296 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: 0:00:01.296 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.299 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.299 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.299 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:01.299 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.299 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.299 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: 0:00:01.299 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.303 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.303 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.303 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (3 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:01.303 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.303 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.303 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: 0:00:01.303 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.307 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.307 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.307 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (3 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:01.307 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.307 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.307 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: 0:00:01.307 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.311 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (3 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:01.311 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.311 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.311 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: 0:00:01.311 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.314 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (3 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:01.315 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.315 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.315 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: 0:00:01.315 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.318 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (3 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:01.319 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.319 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.319 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: 0:00:01.319 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.322 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (3 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:01.323 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.323 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.323 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: 0:00:01.323 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.327 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:01.327 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.327 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.327 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: 0:00:01.327 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.331 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (3 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:01.331 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.331 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.331 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: 0:00:01.331 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.334 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.334 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.334 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (3 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:01.335 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.335 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.335 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: 0:00:01.335 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.338 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.338 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.338 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (3 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:01.338 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.338 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.338 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: 0:00:01.338 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.342 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.342 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.342 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (3 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:01.342 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.342 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.342 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: 0:00:01.342 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.346 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.346 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.346 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (3 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:01.346 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.346 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.346 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: 0:00:01.346 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.349 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.349 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.349 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (3 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:01.350 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.350 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.350 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: 0:00:01.350 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.353 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.353 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 117) Marking start/end overlaps 2: 0:00:01.353 4M / 159M INFO OverlapRemover (overlap_remover.hpp : 120) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (3 ms) 2: [----------] 23 tests from OverlapRemoval (77 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:01.353 1M / 159M INFO General (graph_alignment_test.cpp : 31) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:01.353 1M / 159M INFO General (graph_alignment_test.cpp : 61) Edlib: Result status = 0 2: 0:00:01.353 1M / 159M INFO General (graph_alignment_test.cpp : 63) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:01.353 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.354 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.354 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: 0:00:01.354 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.357 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.357 4M / 159M INFO BWAIndex (bwa_index.cpp : 52) Setting BWA alignment mode to 'pacbio' 2: 0:00:01.360 5M / 159M INFO General (bwa_index.cpp : 150) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (316 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:01.670 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.670 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.670 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: 0:00:01.670 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.674 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (4 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:01.674 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.674 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.674 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: 0:00:01.674 1M / 159M INFO General (graphio.cpp : 50) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.678 4M / 159M INFO General (graphio.cpp : 139) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (3 ms) 2: [----------] 5 tests from GraphAligner (324 ms total) 2: 2: [----------] 1 test from VariableOverlaps 2: [ RUN ] VariableOverlaps.BasicOperations 2: 0:00:01.678 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.678 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: 0:00:01.681 1M / 159M INFO GraphCore (graph_core.hpp : 689) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.681 1M / 159M INFO GraphCore (graph_core.hpp : 690) Vertex size: 48, edge size: 40 2: [ OK ] VariableOverlaps.BasicOperations (5 ms) 2: [----------] 1 test from VariableOverlaps (5 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 100 tests from 11 test suites ran. (1684 ms total) 2: [ PASSED ] 100 tests. 2/2 Test #2: debruijn_test .................... Passed 1.70 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.85 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/rna_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/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/pe_params.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/sewage_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/distance_estimation.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/simplification.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/construction.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_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/rnaviral_mode.info -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.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/biosynthetic_spades_hmms/KR.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/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/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/scaffold_correction_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/pipeline.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/error_correction_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/check_test_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/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/__init__.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/terminating_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/spades_iteration_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/stages/before_start_stage.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/common/alignment.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/executors -- 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/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/support.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/options_storage.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/copy_files.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/correction_iteration_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/spades_pipeline/scripts/check_test_script.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/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/genes_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/reproducible-path/spades-4.0.0+dfsg1/debian/spades/usr/bin/spades-gmapper -- 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-dbgsym' in '../spades-dbgsym_4.0.0+dfsg1-2_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_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: 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/2995195 and its subdirectories I: Current time: Mon Feb 17 12:47:32 -12 2025 I: pbuilder-time-stamp: 1739839652