I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 15 10:18:40 +14 2024 I: pbuilder-time-stamp: 1734207520 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_3.15.5+dfsg-8.dsc] I: copying [./spades_3.15.5+dfsg.orig.tar.xz] I: copying [./spades_3.15.5+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 13 23:10:06 2024 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./spades_3.15.5+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting spades in spades-3.15.5+dfsg dpkg-source: info: unpacking spades_3.15.5+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.15.5+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-gcc13.patch dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0003_accept-system-bwa.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 0103_use-debian-packaged-bwa.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 fix-sigill-on-non-popcnt-cpus.patch dpkg-source: info: applying fix-privacy-breaches.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying python3.12.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/1319961/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 14 20:19 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=17c6d745f6534ab3ba7a44cd04acd76c LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1319961 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qh9ISrsk/pbuilderrc_xYzt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qh9ISrsk/b2 --logfile b2/build.log spades_3.15.5+dfsg-8.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) 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/1319961/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, clang-format, clang-tidy, clang-tools, cmake, python3-all, zlib1g-dev, libbz2-dev, libbam-dev, libbamtools-dev, libc++-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, libzstd-dev, llvm-dev, python3-yaml, python3-joblib, asciidoctor, bwa, libbwa-dev, lynx dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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 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 python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev 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 libc++-dev; however: Package libc++-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 libssw-dev; however: Package libssw-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 python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-joblib; however: Package python3-joblib is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on bwa; however: Package bwa is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on lynx; however: Package lynx 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} bwa{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} 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} libbrotli-dev{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libc++-19-dev{a} libc++-dev{a} libc++1-19{a} libc++abi-19-dev{a} libc++abi1-19{a} libclang-common-19-dev{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{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} libfile-stripnondeterminism-perl{a} libgc1{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{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-2.5-0{a} libldap-dev{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} 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} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libssw-dev{a} libssw0{a} libtasn1-6-dev{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libunbound8{a} libunwind-19{a} libunwind-19-dev{a} libuv1t64{a} libxml2{a} libxml2-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} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{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 python3-simplejson systemd zip 0 packages upgraded, 201 newly installed, 0 to remove and 0 not upgraded. Need to get 224 MB of archives. After unpacking 1154 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 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 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 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 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-2 [858 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-2 [2198 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.5-1 [13.2 MB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.8-1 [247 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14.2.0-8 [42.5 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libobjc-14-dev amd64 14.2.0-8 [170 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libclang-common-19-dev amd64 1:19.1.5-1 [739 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 llvm-19-linker-tools amd64 1:19.1.5-1 [1260 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.5-1 [7615 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 clang-19 amd64 1:19.1.5-1 [116 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 clang-format-19 amd64 1:19.1.5-1 [92.1 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 clang-format amd64 1:19.0-63 [6352 B] Get: 75 http://deb.debian.org/debian unstable/main amd64 clang-tools-19 amd64 1:19.1.5-1 [8955 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 clang-tidy-19 amd64 1:19.1.5-1 [1883 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 clang-tidy amd64 1:19.0-63 [6116 B] Get: 79 http://deb.debian.org/debian unstable/main amd64 clang-tools amd64 1:19.0-63 [6164 B] Get: 80 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.2-1 [2267 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.2-1 [11.9 MB] Get: 95 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2~rc1-2 [55.4 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 102 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 114 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-6+b1 [222 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libunwind-19 amd64 1:19.1.5-1 [62.4 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libc++abi1-19 amd64 1:19.1.5-1 [105 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libc++1-19 amd64 1:19.1.5-1 [302 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libc++abi-19-dev amd64 1:19.1.5-1 [127 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libunwind-19-dev amd64 1:19.1.5-1 [80.9 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libc++-19-dev amd64 1:19.1.5-1 [1285 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libc++-dev amd64 1:19.0-63 [6056 B] Get: 140 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1 [474 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2+b1 [351 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-6+b1 [178 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-6+b1 [46.8 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-6+b1 [205 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-6+b1 [13.5 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [1975 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b1 [21.8 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-15+b1 [24.6 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.13.3-1 [107 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 llvm-19-runtime amd64 1:19.1.5-1 [550 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 llvm-runtime amd64 1:19.0-63 [5904 B] Get: 191 http://deb.debian.org/debian unstable/main amd64 llvm-19 amd64 1:19.1.5-1 [16.4 MB] Get: 192 http://deb.debian.org/debian unstable/main amd64 llvm amd64 1:19.0-63 [8328 B] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 llvm-19-tools amd64 1:19.1.5-1 [510 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 llvm-19-dev amd64 1:19.1.5-1 [43.2 MB] Get: 196 http://deb.debian.org/debian unstable/main amd64 llvm-dev amd64 1:19.0-63 [6152 B] Get: 197 http://deb.debian.org/debian unstable/main amd64 lynx-common all 2.9.2-1 [1193 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 lynx amd64 2.9.2-1 [641 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-2 [740 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-5 [216 kB] Fetched 224 MB in 12s (18.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... 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 python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... 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 ... 20285 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_amd64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... 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 .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-6_amd64.deb ... 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 libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_amd64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (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 ... 21348 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_amd64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. 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Setting up libffi-dev:amd64 (3.4.6-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Dec 14 20:21:31 UTC 2024. Universal Time is now: Sat Dec 14 20:21:31 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:amd64 (3.13.1-2) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libpfm4:amd64 (4.13.0+git83-g91970fe-1) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libncurses6:amd64 (6.5-2+b1) ... 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Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up python3.13-minimal (3.13.1-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up cmake-data (3.31.2-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up lynx (2.9.2-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libunwind-19-dev:amd64 (1:19.1.5-1) ... Setting up libnlopt-dev:amd64 (2.7.1-6+b1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up openssl (3.3.2-2) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up libssw0:amd64 (1.1-15+b1) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:amd64 (72.1-5+b1) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libllvm19:amd64 (1:19.1.5-1) ... Setting up libz3-dev:amd64 (4.13.3-1) ... Setting up libncurses-dev:amd64 (6.5-2+b1) ... Setting up gettext (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up libclang1-19 (1:19.1.5-1) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libc++abi-19-dev:amd64 (1:19.1.5-1) ... Setting up libssw-dev:amd64 (1.1-15+b1) ... Setting up libtool (2.4.7-8) ... Setting up libobjc4:amd64 (14.2.0-8) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... Setting up libobjc-14-dev:amd64 (14.2.0-8) ... Setting up libngtcp2-dev:amd64 (1.9.1-1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libc++-19-dev:amd64 (1:19.1.5-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libnlopt-cxx-dev:amd64 (2.7.1-6+b1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-6+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up llvm-19-linker-tools (1:19.1.5-1) ... Setting up llvm-19-runtime (1:19.1.5-1) ... Setting up libc++-dev:amd64 (1:19.0-63) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... Setting up libclang-cpp19 (1:19.1.5-1) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up clang-19 (1:19.1.5-1) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up llvm-runtime:amd64 (1:19.0-63) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.31.2-1) ... Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up llvm-19 (1:19.1.5-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.20) ... Setting up llvm (1:19.0-63) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up clang-tools-19 (1:19.1.5-1) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up clang-tools:amd64 (1:19.0-63) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up clang-format-19 (1:19.1.5-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up clang-format:amd64 (1:19.0-63) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-joblib (1.3.2-5) ... Setting up clang-tidy-19 (1:19.1.5-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up llvm-19-tools (1:19.1.5-1) ... Setting up dh-python (6.20241024) ... Setting up clang-tidy (1:19.0-63) ... Setting up llvm-19-dev (1:19.1.5-1) ... Setting up llvm-dev (1:19.0-63) ... Setting up rake (13.2.1-1) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-8_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.5+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=assembler/src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_clean find . -name "*.pyc" -delete rm -rf /build/reproducible-path/spades-3.15.5+dfsg/debian/man_src/*.html /build/reproducible-path/spades-3.15.5+dfsg/debian/man_src/*.? rm -rf /build/reproducible-path/spades-3.15.5+dfsg/debian/man make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_autoreconf_clean -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_clean -X.orig make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' debian/rules binary dh binary --sourcedirectory=assembler/src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_configure -- -DBoost_NO_BOOST_CMAKE=TRUE 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 ../assembler/src CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as project(ProjectName) near the top of the file, but after cmake_minimum_required(). CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in CMakeLists.txt: cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- 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 OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- 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:30 (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: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include 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:55 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/deps.cmake:30 (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:55 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include (found version "1.63.0") Making Release Configuration... Building SPAdes from N/A, sha: N/A CMake Deprecation Warning at /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-none -- Build type : none -- Compiler : /usr/bin/c++ -- Install directory: /usr/lib/mimalloc-1.6 -- Build targets : object -- -- 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 unistd.h -- Looking for unistd.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 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 "8.11.1") -- 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 stdint.h -- Looking for include file stdint.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.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 emmintrin.h -- Looking for include file emmintrin.h - found -- Looking for include file pmmintrin.h -- Looking for include file pmmintrin.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for chmod -- Looking for chmod - found -- Looking for fseeko -- Looking for fseeko - found -- Looking for fstat -- Looking for fstat - found -- Looking for getcwd -- Looking for getcwd - found -- Looking for getpid -- Looking for getpid - found -- Looking for mkstemp -- Looking for mkstemp - found -- Looking for popen -- Looking for popen - found -- Looking for putenv -- Looking for putenv - found -- Looking for stat -- Looking for stat - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for sysctl -- Looking for sysctl - not found -- Looking for times -- Looking for times - found -- Looking for erfc -- Looking for erfc - not found CMake Deprecation Warning at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/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. CMake Deprecation Warning at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/CMakeLists.txt:56 (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. CMake Warning (dev) at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/cmake/internal_utils.cmake:247 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/CMakeLists.txt:91 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found version "3.12.8") CMake Deprecation Warning at projects/mts/CMakeLists.txt:8 (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. -- Configuring done (51.9s) -- Generating done (0.9s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_build -- all debruijn_test include_test cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake "--color=" make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o [ 1%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -MF CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o.d -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/PairwiseAlignment.cpp [ 1%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 1%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/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-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/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-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp [ 3%] Building C object ext/easel/CMakeFiles/easel.dir/easel.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.c [ 3%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/version.cpp [ 3%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp [ 4%] Linking CXX static library libversion.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:610:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 610 | printf("%02llx ", j); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:641:20: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 642 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:641:25: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 642 | qf->metadata->nblocks, 643 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:641:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 641 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 644 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_deserialize': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1606:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1606 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1615:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1615 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target version make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 4%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -MF CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o.d -o CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp [ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -MF CMakeFiles/ConsensusCore.dir/Utils.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:466:15: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'mem_region_t' {aka 'struct mem_region_s'} with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] 466 | memset(®ions[i], 0, sizeof(mem_region_t)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:89:16: note: 'mem_region_t' {aka 'struct mem_region_s'} declared here 89 | typedef struct mem_region_s { | ^~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c: In function 'mi_heap_t* mi_heap_new()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c:196:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] 196 | memcpy(heap, &_mi_heap_empty, sizeof(mi_heap_t)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-internal.h:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:17: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc.c:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c: At global scope: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:71:42: note: in expansion of macro 'MI_FORWARD1' 71 | void* malloc(size_t size) MI_FORWARD1(mi_malloc, size); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:72:42: note: in expansion of macro 'MI_FORWARD2' 72 | void* calloc(size_t size, size_t n) MI_FORWARD2(mi_calloc, size, n); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:73:42: note: in expansion of macro 'MI_FORWARD2' 73 | void* realloc(void* p, size_t newsize) MI_FORWARD2(mi_realloc, p, newsize); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:95:55: note: in expansion of macro 'MI_FORWARD1' 95 | void* operator new(std::size_t n) noexcept(false) MI_FORWARD1(mi_new,n); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:96:55: note: in expansion of macro 'MI_FORWARD1' 96 | void* operator new[](std::size_t n) noexcept(false) MI_FORWARD1(mi_new,n); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:167:42: note: in expansion of macro 'MI_FORWARD2' 167 | void* reallocf(void* p, size_t newsize) MI_FORWARD2(mi_reallocf,p,newsize); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:168:42: note: in expansion of macro 'MI_FORWARD1' 168 | size_t malloc_size(const void* p) MI_FORWARD1(mi_usable_size,p); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:170:42: note: in expansion of macro 'MI_FORWARD1' 170 | size_t malloc_usable_size(void *p) MI_FORWARD1(mi_usable_size,p); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:29:35: note: in expansion of macro 'MI_FORWARD' 29 | #define MI_FORWARD1(fun,x) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:194:53: note: in expansion of macro 'MI_FORWARD1' 194 | void* __libc_malloc(size_t size) MI_FORWARD1(mi_malloc,size); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:195:53: note: in expansion of macro 'MI_FORWARD2' 195 | void* __libc_calloc(size_t count, size_t size) MI_FORWARD2(mi_calloc,count,size); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:25:101: warning: 'nodiscard' attribute directive ignored [-Wattributes] 25 | #define MI_FORWARD(fun) __attribute__((alias(#fun), used, visibility("default"), copy(fun))) | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:30:35: note: in expansion of macro 'MI_FORWARD' 30 | #define MI_FORWARD2(fun,x,y) MI_FORWARD(fun) | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] 192 | memcpy(heap, &_mi_heap_empty, sizeof(*heap)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ [ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o -MF CMakeFiles/ConsensusCore.dir/Version.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Version.cpp [ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_alphabet.c [ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp [ 5%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp [ 5%] Linking C static library libgqf.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c [ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp [ 5%] Linking CXX static library libgetopt_pp.a [ 5%] Built target gqf cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 [ 5%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp [ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o /usr/bin/ranlib libgetopt_pp.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 5%] Built target getopt_pp [ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -MF CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp [ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp [ 6%] Linking C static library libgfa1.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 /usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o /usr/bin/ranlib libgfa1.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 8%] Linking CXX static library libedlib.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake [ 8%] Built target gfa1 [ 8%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp [ 8%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 8%] Built target edlib make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 8%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp [ 8%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ [ 8%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? | ^~~~~~~ [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here 207 | graph_io_.Load(basename, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:210:45: required from here 210 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:213:34: required from here 213 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:216:35: required from here 216 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here 219 | loader.Load>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here 253 | graph_io_.BinRead(is, gp.get_mutable()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here 256 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:259:34: required from here 259 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here 262 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here 265 | reader.Read>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ [ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c [ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamReader.cpp [ 9%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamWriter.cpp [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c [ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gamma.c.o -MF CMakeFiles/easel.dir/esl_gamma.c.o.d -o CMakeFiles/easel.dir/esl_gamma.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gamma.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' 97 | DeleteLink(w, e2); | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here 109 | helper.LinkEdges(e1, e2); | ~~~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c [ 11%] Linking CXX static library libformat.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c [ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c [ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgram.cpp /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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 12%] Built target format make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 13%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/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-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c [ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c [ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroup.cpp [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 16%] Built target mimalloc-obj make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 16%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp [ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c [ 19%] Linking CXX static library libsequence.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P 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-Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o /usr/bin/ranlib libsequence.a [ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp [ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c [ 19%] Built target sequence [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp [ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c [ 20%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_a2m.c.o -MF CMakeFiles/easel.dir/esl_msafile_a2m.c.o.d -o CMakeFiles/easel.dir/esl_msafile_a2m.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_a2m.c [ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp [ 20%] Linking CXX static library libcoverage_model.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 [ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/bin/ar qc 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-3.15.5+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 22%] Built target coverage_model [ 22%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp [ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/vector:63, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_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-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp [ 25%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp [ 26%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' 578 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ [ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/JSON.cpp [ 27%] Linking CXX static library libmapping_printer.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] 344 | fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", | ~~~^ | | | long long int | %ld 345 | q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); | ~~~~~ | | | int64_t {aka long int} In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h: At top level: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c /usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o /usr/bin/ranlib libmapping_printer.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 29%] Built target mapping_printer [ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c [ 29%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c [ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_random.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp [ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c [ 31%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp [ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp [ 32%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp [ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c [ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c [ 33%] Linking CXX static library libgraphio.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c [ 34%] Built target graphio [ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp [ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c [ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:23: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c: In function 'esl_scorematrix_Create': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:166:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 166 | if ( ((p) = malloc(size)) == NULL) { \ | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c:72:3: note: in expansion of macro 'ESL_ALLOC' 72 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.h:23: /usr/include/stdlib.h:672:14: note: in a call to allocation function 'malloc' declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c [ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c [ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c [ 37%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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-3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c [ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c [ 38%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o cd 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ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o [ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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&& /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 [ 40%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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/usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib libBamTools.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp [ 41%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp [ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_aux.c [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp [ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c [ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ~~~~~~~~~~^~ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: /usr/include/malloc.h:114:24: note: declared here 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ [ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp [ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_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-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Linking C static library libeasel.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD 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CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_vmx.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o /usr/bin/ranlib libeasel.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 44%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build make[4]: Entering 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ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp [ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c [ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/cachedb.c [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -MF CMakeFiles/hmmer.dir/src/emit.c.o.d -o CMakeFiles/hmmer.dir/src/emit.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/emit.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp [ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/errors.c [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp [ 48%] Linking CXX static library libpaired_info.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake [ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/evalues.c [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 [ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bedidx.c [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 48%] Built target paired_info [ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd 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CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c [ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam_header.c [ 50%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp [ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/eweight.c [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c [ 51%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd 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CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c [ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c [ 51%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c [ 51%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 51%] Built target utils [ 52%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c [ 52%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c [ 52%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_fwdback.c [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_fwdback_chk.c [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_fwdback_banded.c [ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_null2.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_msv.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_optacc.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_stotrace.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -MF CMakeFiles/hmmer.dir/src/generic_viterbi.c.o.d -o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_viterbi.c [ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_vtrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_vtrace.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/h2_io.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/heatmap.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c [ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o cd 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdutils.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmer.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelconfig.c [ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/mpisupport.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c [ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_builder.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gbands.c [ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxchk.c [ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmwindow.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_null3.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_pipeline.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_prior.c [ 60%] Linking CXX static library libsamtools.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_profile.c [ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_tophits.c.o -MF CMakeFiles/hmmer.dir/src/p7_tophits.c.o.d -o CMakeFiles/hmmer.dir/src/p7_tophits.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_tophits.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o -MF CMakeFiles/hmmer.dir/src/p7_trace.c.o.d -o CMakeFiles/hmmer.dir/src/p7_trace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_trace.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o /usr/bin/ranlib libsamtools.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_scoredata.c make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 61%] Built target samtools [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -MF CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o.d -o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmpgmd2msa.c In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, inlined from 'void omnigraph::de::Histogram::BinArchiveLoad(Archive&) [with Archive = io::binary::impl::StreamArchiveReader; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:200:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::Histogram::BinArchiveLoad(Archive&) [with Archive = io::binary::impl::StreamArchiveReader; Point = omnigraph::de::PointT]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -MF CMakeFiles/hmmer.dir/src/fm_alphabet.c.o.d -o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_alphabet.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_general.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/decoding.c [ 62%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::RawPointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::RawPointT&}; T = omnigraph::de::RawPointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::RawPointT&; Args = {}; T = omnigraph::de::RawPointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::RawPointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::RawPointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, inlined from 'void omnigraph::de::Histogram::BinArchiveLoad(Archive&) [with Archive = io::binary::impl::StreamArchiveReader; Point = omnigraph::de::RawPointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:200:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::RawPointT [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::Histogram::BinArchiveLoad(Archive&) [with Archive = io::binary::impl::StreamArchiveReader; Point = omnigraph::de::RawPointT]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 8 into object 'tmp' of size 8 580 | value_type tmp(std::forward(args)...); | ^~~ [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_omx.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c [ 65%] Linking CXX static library libConsensusCore.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o /usr/bin/ranlib libConsensusCore.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/io/binary/binary.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/io_base.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:9: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 65%] Built target ConsensusCore make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp [ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp [ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o [ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp [ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp [ 67%] Linking CXX static library ../../../lib/libgtest.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 [ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp /usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" /usr/bin/ranlib ../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target gtest make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o [ 68%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 68%] Linking CXX static library ../../../lib/libgtest_main.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o /usr/bin/ranlib ../../../lib/libgtest_main.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 68%] Built target gtest_main [ 68%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 68%] Linking CXX static library libllvm-support.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/is_counter.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 69%] Linking CXX static library libteamcity_gtest.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 69%] Built target teamcity_gtest [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 235 | if (data.median_insert_size < gp.k() + 2) | ~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 216 | for (;index != res.first; ++index) { | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 243 | if (coords.second + 5000 > path.Length()) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] 457 | bool u1 = UpdateLeft(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] 458 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, long unsigned int>]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:103:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' 103 | std::vector common_part = GetCommonPathsEnd(graph_, cur_edge, cur_info.second, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 104 | (size_t) (cur_info.d() - cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 | (size_t) (cur_info.d() + cur_info.var()), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 | dijkstra); | ~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:230:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 230 | auto paths = spc.ConvertPIToSplitPaths(*e, index_, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 231 | lib_.data().mean_insert_size, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | lib_.data().insert_size_deviation); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:102:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 102 | missing_paired_info_count = FillMissing(nthreads); | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:93:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' 93 | CorrectPairedInfo(num_threads); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:165:31: required from here 165 | improver.ImprovePairedInfo((unsigned) config.max_threads); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 28 | size_t min_dist, | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 72%] Linking C static library libhmmer.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o /usr/bin/ranlib libhmmer.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target hmmer make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here 362 | for (auto edge = g_.SmartEdgeBegin(); !edge.IsEnd(); ++edge) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ [ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:20: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp:7, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 72%] Linking CXX static library libbinary_io.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 /usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o /usr/bin/ranlib libbinary_io.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target binary_io make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 123 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here 394 | omnigraph::CompressAllVertices(g_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ [ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp [ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 161 | pli->Z = pli->domZ = cfg.Z; | ~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 72%] Linking CXX static library libhmmercpp.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /usr/bin/ranlib libhmmercpp.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target hmmercpp [ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp [ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 123 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here 722 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp [ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/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-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:163:21: required from 'void utils::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' 163 | data_.resize(sz); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:43:21: required from 'void utils::PerfectHashMapBuilder::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' 43 | index.resize(storage.total_kmers()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:144:39: required from 'void utils::BuildIndex(PerfectHashMap&, const KMerStorage&, size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' 144 | PerfectHashMapBuilder().BuildIndex(index, storage, thread_num); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:249:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' 249 | BuildIndex(index, storage, nthreads); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:27:39: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' 27 | IndexBuilder().BuildIndexFromGraph(index, g); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:31:64: required from here 31 | void EdgeIndexRefiller::Refill(EdgeIndex &index, const Graph &g); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 20 | IdHolder edge_id_; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/alloc_traits.h:39, from /usr/include/c++/14/ext/alloc_traits.h:34, from /usr/include/c++/14/bits/hashtable_policy.h:39, from /usr/include/c++/14/bits/hashtable.h:35, from /usr/include/c++/14/bits/unordered_map.h:33, from /usr/include/c++/14/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_set_params, std::allocator, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node, std::allocator, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_set_params, std::allocator, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp [ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, inlined from 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_filters.hpp:257:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void omnigraph::de::PairInfoFilter::Filter(omnigraph::de::PairedInfoIndexT&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:10: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/streambuf:43, from /usr/include/c++/14/bits/streambuf_iterator.h:35, from /usr/include/c++/14/iterator:66, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/iterator/iterator_facade.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/chained_iterator.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = nrps::DomainGraphDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 74%] Linking CXX static library libinput.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target input In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:168:43: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, inlined from 'std::pair::iterator, bool> adt::flat_set::insert(const value_type&) [with T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:62:79, inlined from 'std::pair, adt::SmallPODVector>::iterator, bool> omnigraph::de::Histogram::insert(const value_type&) [with Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:97:79, inlined from 'typename std::enable_if<(! omnigraph::de::Histogram::can_merge::value), long unsigned int>::type omnigraph::de::Histogram::merge_point(const U&) [with U = omnigraph::de::PointT; Point = omnigraph::de::PointT]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:160:29, inlined from 'std::pair, G, Traits>::InnerPoint> >::pointer, long unsigned int> omnigraph::de::PairedBuffer::InsertOne(typename base::EdgeId, typename base::EdgeId, typename base::InnerPoint) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:246:47, inlined from 'void omnigraph::de::PairedBufferBase::InsertWithConj(EdgeId, EdgeId, InnerPoint) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:108:58, inlined from 'void omnigraph::de::PairedBufferBase::Add(EdgeId, EdgeId, Point) [with Derived = omnigraph::de::PairedBuffer; G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:56:23, inlined from 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:170:43: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 16 is outside array bounds of 'adt::SmallPODVector >::value_type [1]' {aka 'omnigraph::de::PointT [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void debruijn_graph::PairInfoImprover::ContradictionalRemover::FindInconsistent(debruijn_graph::PairInfoImprover::EdgeId, debruijn_graph::PairInfoImprover::Index&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ [ 74%] Linking CXX static library libassembly_graph.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/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-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/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-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -MF CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o [ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o [ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp [ 79%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp:14, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/ideal_pair_info.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here 34 | for (auto it = g.SmartVertexBegin(); ! it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here 131 | for (auto iter = graph.SmartEdgeBegin(); ! iter.IsEnd(); ++iter) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 29 | if (sum < absolute_weight_threshold_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here 597 | virtual void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:7, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:3, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:3, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:34:13: note: in expansion of macro 'SET_PRIORITY' 34 | SET_PRIORITY(LibraryType::SangerReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' 46 | SET_PRIORITY(LibraryType::AssemblyGraph); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 111 | if (iter->second < min_read_count_) { | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:12: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 81%] Linking CXX static library libmodules.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 [ 81%] Linking CXX static library libspades-stages.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target modules [ 81%] Linking CXX static library libpath_extend.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target spades-stages /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 82%] Linking CXX static library libpipeline.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/cmake -E cmake_link_script CMakeFiles/pipeline.dir/link.txt --verbose=1 /usr/bin/ar qc libpipeline.a CMakeFiles/pipeline.dir/config_struct.cpp.o CMakeFiles/pipeline.dir/graph_pack.cpp.o CMakeFiles/pipeline.dir/library.cpp.o CMakeFiles/pipeline.dir/library_data.cpp.o CMakeFiles/pipeline.dir/stage.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[4]: Entering directory 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-f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/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-3.15.5+dfsg/assembler/src/common/stages/read_conversion.cpp [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o 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-std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp [ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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-3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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-3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp [ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 26 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 28 | num_flows = measurements.size(); | ~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] 46 | unsigned int prefix_size = master_read.sequence.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 85 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:86:63: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 86 | transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:97:45: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 97 | int num_flows = read.raw_measurements.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:127:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 127 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:166:52: warning: conversion from 'int' to 'float' may change value [-Wconversion] 166 | float delta = (next_normalizer - normalizer) / window_size; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:350:38: warning: conversion from 'double' to 'float' changes value from '1.0e+20' to '1.00000002e+20f' [-Wfloat-conversion] 350 | float sum_of_squares_upper_bound = 1e20; //max_flows; // Squared distance of solution to measurements | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:409:35: warning: conversion from 'double' to 'float' changes value from '-1.0000000000000001e-1' to '-1.00000001e-1f' [-Wfloat-conversion] 409 | float max_per_flow_metric = -0.1; | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:514:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 514 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] 292 | int backward_idx = seq.size()-1; | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hkmer.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:16, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:175:52: required from 'void kmers::KMerDiskStorage::merge() [with S = hammer::HSeq<16>; traits = kmers::kmer_index_traits >]' 175 | BucketStorage bucket(*entry, Seq::GetDataSize(k_), false); | ~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:446:25: required from 'auto kmers::KMerIndexBuilder::BuildIndex(Index&, kmers::KMerCounter&, bool) [with Index = kmers::KMerIndex > >; typename Index::KMerSeq = hammer::HSeq<16>]' 446 | kmer_storage.merge(); | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:172:102: required from here 172 | auto res = kmers::KMerIndexBuilder(num_files_, cfg::get().max_nthreads).BuildIndex(data.index_, counter, false); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/HSeq.hpp:93:36: warning: unused parameter 'size' [-Wunused-parameter] 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:357:110: required from here 357 | DeBruijnGraphExtentionConstructor(gp.get_mutable(), storage().ext_index).ConstructGraph(storage().params.keep_perfect_loops); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] 90 | } | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = adt::identity; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 59 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:328:94: required from here 328 | SelfConjugateDisruptor(g_, cfg::get().max_repeat_length, removal_handler_).Run(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:345:28: required from here 345 | cov_cleaner.Run(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 123 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here 474 | CompressAllVertices(gp.get_mutable()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 59 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 38 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 56 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:83:52: required from here 83 | bool changed = TopologyRemoveErroneousEdges(g_, simplif_cfg_.tec, handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:17: /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:100:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 100 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:94:33: required from 'omnigraph::GraphComponent omnigraph::ComplexTipFinder::operator()(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 94 | if (finder.FillDominated()) { | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:149:49: required from 'omnigraph::ComplexTipClipper::ComplexTipClipper(Graph&, double, size_t, size_t, size_t, const std::string&, HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; std::string = std::__cxx11::basic_string; HandlerF = std::function, std::allocator >&)>]' 149 | [&](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:694:19: [ 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-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:492:65: 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 >&)>]' 492 | return std::make_shared>(g, ctc_conf.max_relative_coverage, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 493 | ctc_conf.max_edge_len, | ~~~~~~~~~~~~~~~~~~~~~~ 494 | parser.max_length_bound(), info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | "", removal_handler); | ~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:248:42: required from here 248 | ComplexTipClipperInstance(g_, simplif_cfg_.complex_tc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 83 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 504 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 667 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: 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::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' 720 | [&](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&, __cxx11::basic_string, allocator >&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ 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::__cxx11::basic_string, 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&, 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::__cxx11::basic_string, std::allocator >&}; _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::__cxx11::basic_string, std::allocator >&}; _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&, __cxx11::basic_string, allocator >&}; 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-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: 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 >&)>]' 430 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 432 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 433 | flanking_cov, | ~~~~~~~~~~~~~ 434 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 435 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 | max_coverage, | ~~~~~~~~~~~~~ 439 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:237:57: required from here 237 | RelativeCoverageComponentRemoverInstance(g_, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 238 | simplif_cfg_.rcc, info_container_, set_removal_handler_f), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 720 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here 677 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 813 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1121 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: 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]' 1149 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1195 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here 1189 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:777:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 777 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:824:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 824 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1121 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: 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]' 1149 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1195 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here 1189 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here 309 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] 309 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:320:10: required from here 320 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:322:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 322 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:18: required from here 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:71: warning: unused parameter 'edge2' [-Wunused-parameter] 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:241:18: required from here 241 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 86%] Linking CXX executable ../../bin/spades-ionhammer cd /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -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/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a /usr/lib/x86_64-linux-gnu/libz.so ../../common/io/binary/libbinary_io.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 -lssw ../../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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target spades-ionhammer /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:12: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 86%] Linking CXX static library libstages.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] Building CXX object common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/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-3.15.5+dfsg/assembler/src/common/adt/concurrent_dsu.cpp [ 86%] Linking CXX static library libcommon_modules.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target common_modules make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake "--color=" make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend [ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/main.cpp [ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend [ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o [ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o [ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o [ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/main.cpp [ 88%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/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-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp [ 88%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o [ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp [ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o [ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp [ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 89%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -MF CMakeFiles/spades-gmapper.dir/main.cpp.o.d -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp [ 89%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp [ 89%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp [ 90%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] 135 | pipeline_type mode = cfg::get().mode; | ^~~~ [ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' 543 | vm.Start(vals, num_elems, num_threads); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' 54 | PairSort::InitAndSort(data.data(), blocks.data(), data.size(), data.size() > 1000*16 ? -1 : 1); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here 147 | Splitter.split([&] (const std::vector::iterator &start, size_t sz) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | if (sz < block_thr) { | ~~~~~~~~~~~~~~~~~~~~~ 149 | // Merge small blocks. | ~~~~~~~~~~~~~~~~~~~~~~ 150 | processBlockQuadratic(uf, start, sz, data, tau_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 | } else { | ~~~~~~~~ 152 | big_blocks1 += 1; | ~~~~~~~~~~~~~~~~~ 153 | // Otherwise - dump for next iteration. | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 | for (unsigned i = 0; i < tau_ + 1; ++i) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 | serialize(bfs, kfs, | ~~~~~~~~~~~~~~~~~~~ 156 | data, &start, sz, | ~~~~~~~~~~~~~~~~~ 157 | SubKMerStridedSerializer(i, tau_ + 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 | } | ~ 159 | } | ~ 160 | }); | ~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here 197 | debruijn_graph::FastGraphFromSequencesConstructor(k, ext_index).ConstructGraph(g, edge_sequences); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 357 | for (uint32_t j=0; j::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ [ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/spaligner.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 123 | return compressor.Run(); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here 722 | CompressAllVertices(g_, /*chunk_cnt*/100); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp [ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /usr/include/string.h:548, from /usr/include/c++/14/cstring:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/read_processor.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:12: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 6 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 48 into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2895:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 7 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 56 into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2873:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 'long unsigned int[4]' is partly outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [33, 40] into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2896:39, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript [5, 6] is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset [41, 48] into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ In function 'void* memcpy(void*, const void*, size_t)', inlined from 'xxh_u64 XXH_read64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1630:11, inlined from 'xxh_u64 XXH_readLE64(const void*)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:1687:34, inlined from 'xxh_u64 XXH3_mix16B(const xxh_u8*, const xxh_u8*, xxh_u64)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2874:46, inlined from 'XXH64_hash_t XXH3_len_17to128_64b(const xxh_u8*, size_t, const xxh_u8*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:2898:35, inlined from 'XXH64_hash_t XXH3_64bits_internal(const void*, size_t, XXH64_hash_t, const void*, size_t, XXH3_hashLong64_f)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3852:36, inlined from 'XXH64_hash_t XXH_INLINE_XXH3_64bits_withSeed(const void*, size_t, XXH64_hash_t)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/xxh/xxhash.h:3875:32, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:682:36, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:686:23, 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-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:691:31, inlined from 'size_t kmer::KMerSegmentPolicy::operator()(const Seq&) const [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_buckets.hpp:32:45, inlined from 'bool kmers::KMerSortingSplitter::push_back_internal(const Seq&, unsigned int) [with Seq = RuntimeSeq<128>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitter.hpp:115:35, inlined from 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:78:51: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:29:33: warning: array subscript 5 is outside array bounds of 'RtSeq [1]' {aka 'RuntimeSeq<128> [1]'} [-Warray-bounds=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp: In member function 'bool ParallelSortingSplitter::BufferFiller::operator()(std::unique_ptr)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 40 into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ [ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 94%] Linking CXX executable ../../bin/spades-core cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] 103 | const bool using_edge_qual = edge_qual.IsAttached(); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 95%] Linking CXX executable ../../bin/spades-truseq-scfcorrection cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:21: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-truseq-scfcorrection.dir/link.d "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target spades-truseq-scfcorrection [ 96%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 83 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 504 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 667 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: 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::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' 720 | [&](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&, __cxx11::basic_string, allocator >&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ 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::__cxx11::basic_string, 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&, 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::__cxx11::basic_string, std::allocator >&}; _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::__cxx11::basic_string, std::allocator >&}; _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&, __cxx11::basic_string, allocator >&}; 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-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: 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 >&)>]' 430 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 432 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 433 | flanking_cov, | ~~~~~~~~~~~~~ 434 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 435 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 | max_coverage, | ~~~~~~~~~~~~~ 439 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/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-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 720 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here 677 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here 353 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here 353 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here 353 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' [ 96%] Linking CXX executable ../../bin/spades-corrector-core cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-core.dir/link.d "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Linking CXX executable ../../bin/spades-hammer cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 [ 97%] Built target spades-core /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] 248 | EdgeSet ProcessComponent(const VertexSet &reached, | ~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 275 | for (EdgeId e : annotated) { | ^ [ 97%] Linking CXX executable ../../bin/spades-kmer-estimating cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 465 | for (EdgeId e : annotated) { | ^ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-corrector-core.dir/link.d "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-corrector-core /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-hammer.dir/link.d "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-hammer /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-kmer-estimating.dir/link.d "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-kmer-estimating In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-convert-bin-to-fasta.dir/link.d "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-convert-bin-to-fasta /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 98%] Linking CXX executable ../../bin/spades-read-filter cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/unitig-coverage cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-read-filter.dir/link.d "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-read-filter /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitig-coverage.dir/link.d "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target unitig-coverage [ 98%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-kmercount.dir/link.d "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-kmercount /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 98%] Linking CXX executable ../../bin/spades-gmapper cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-gmapper.dir/link.d "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-gmapper /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [ 98%] Linking CXX executable ../../bin/form_truealignments cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 [ 98%] Linking CXX executable ../../bin/spaligner cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/form_truealignments.dir/link.d CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target form_truealignments /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spaligner.dir/link.d CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spaligner /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [100%] Linking CXX executable ../../bin/cds-subgraphs cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cds-subgraphs.dir/link.d "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-subgraphs /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [100%] Linking CXX executable ../../bin/spades-gbuilder cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-gbuilder.dir/link.d "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-gbuilder /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/cds-mapping-stats cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cds-mapping-stats.dir/link.d "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-mapping-stats [100%] Linking CXX executable ../../bin/mag-improve cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/mag-improve.dir/link.d "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target mag-improve [100%] Linking CXX executable ../../bin/spades-gsimplifier cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gsimplifier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/spades-gsimplifier.dir/link.d "CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o" "CMakeFiles/spades-gsimplifier.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gsimplifier ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-gsimplifier make[3]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 debruijn_test make[3]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles 42 make -f CMakeFiles/Makefile2 test/debruijn/CMakeFiles/debruijn_test.dir/all make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest 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Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target gqf Consolidate compiler generated dependencies of target format Consolidate compiler generated dependencies of target version Consolidate compiler generated dependencies of target binary_io make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target gtest make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target mimalloc-obj make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target edlib make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target paired_info Consolidate compiler generated dependencies of target coverage_model make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build Consolidate compiler generated dependencies of target BamTools Consolidate compiler generated dependencies of target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build [ 4%] Built target format [ 7%] Built target version [ 11%] Built target edlib [ 11%] Built target mimalloc-obj [ 11%] Built target gqf [ 4%] Built target binary_io [ 4%] Built target gtest make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 11%] Built target coverage_model Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". [ 14%] Built target paired_info Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". [ 52%] Built target BamTools [ 52%] Built target llvm-support Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" Consolidate compiler generated dependencies of target teamcity_gtest make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target sequence make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/faidx.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target utils [ 52%] Built target teamcity_gtest Consolidate compiler generated dependencies of target samtools make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build [ 54%] Built target sequence make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 57%] Built target utils [ 64%] Built target samtools make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/reads/parser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/read.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target assembly_graph make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build Consolidate compiler generated dependencies of target input make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 69%] Built target assembly_graph [ 73%] Built target input make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target modules make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 78%] Built target modules Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Dependencies file "common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target pipeline make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 90%] 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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" Dependencies file "common/stages/CMakeFiles/stages.dir/construction.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/simplification.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Dependencies file "common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target stages make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" Dependencies file "common/CMakeFiles/common_modules.dir/adt/concurrent_dsu.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target common_modules make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target common_modules make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn/CMakeFiles/debruijn_test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -MF CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -MF CMakeFiles/debruijn_test.dir/test_utils.cpp.o.d -o CMakeFiles/debruijn_test.dir/test_utils.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -MF CMakeFiles/debruijn_test.dir/histogram_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/histogram_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -MF CMakeFiles/debruijn_test.dir/construction_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/construction_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:84:57: required from here 84 | for (auto it = g.SmartVertexBegin(); !it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:24:12: warning: unused variable 'read_count' [-Wunused-variable] 24 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::Point&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:31:12: warning: unused variable 'read_count' [-Wunused-variable] 31 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadGraph(const std::string&, debruijn_graph::Graph&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:70:26: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 70 | VertexId new_id = graph.AddVertex(typename Graph::VertexData(), vid, conj_vid); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:128:24: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 128 | EdgeId new_id = graph.AddEdge(start_id, fin_id, Graph::EdgeData(tmp), eid, conj_eid); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In member function 'bool debruijn_graph::LegacyTextIO::LoadPositions(const std::string&, omnigraph::EdgesPositionHandler&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:193:13: warning: variable 'read_count' set but not used [-Wunused-but-set-variable] 193 | int read_count = fscanf(file, "%zu\n", &pos_count); | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] 415 | ObservableGraph::~ObservableGraph() { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:415:30: note: remove the '< >' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:46:38: required from here 46 | for (size_t i = 0; i < 5; ++i, ++it) | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' 33 | ++it1; | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here 63 | CompareGraphIterators(graph.SmartEdgeBegin(), new_graph.SmartEdgeBegin()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 104 | gap_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 115 | ends_cfg.penalty_ratio = 0.1; | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 153 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 183 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 191 | gap_cfg.penalty_ratio = 0.1; | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:48:62: required from 'debruijn_graph::RandomGraphAccessor::EdgeId debruijn_graph::RandomGraphAccessor::GetRandomEdge() const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 48 | for (auto it = graph_.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:173:48: required from 'void debruijn_graph::RandomPairedIndex::RemoveRandomEdgeInfo() [with Index = omnigraph::de::PairedIndex]' 173 | this->value_.Remove(this->GetRandomEdge()); | ~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:184:13: required from 'void debruijn_graph::RandomPairedIndex::PerformRandomOperation() [with Index = omnigraph::de::PairedIndex]' 184 | RemoveRandomEdgeInfo(); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:176:10: required from here 176 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:40:13: required from 'debruijn_graph::RandomGraphAccessor::VertexId debruijn_graph::RandomGraphAccessor::GetRandomVertex() const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 40 | ++it; | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:100:51: required from 'void debruijn_graph::RandomGraph::AddRandomEdge() [with Graph = debruijn_graph::DeBruijnGraph]' 100 | this->value_.AddEdge(this->GetRandomVertex(), this->GetRandomVertex(), | ~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' 119 | AddRandomEdge(); | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here 112 | void PerformRandomOperation() override { | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' 59 | g_c.ConstructGraph(params.keep_perfect_loops); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' 77 | KMerFiles kmers = ConstructGraph(params, workdir, streams, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here 75 | ConstructGraphWithIndex(config::debruijn_config::construction(), workdir, streams, graph, index); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:125:55: required from here 125 | for (auto it = g.SmartEdgeBegin(); !it.IsEnd(); ++it) { | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' 547 | FastGraphFromSequencesConstructor(kmer_size_, origin_).ConstructGraph(graph_, edge_sequences); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' 59 | g_c.ConstructGraph(params.keep_perfect_loops); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' 68 | return ConstructGraphUsingExtensionIndex(params, workdir, streams, g); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here 138 | ConstructGraph(config::debruijn_config::construction(), workdir, streams, g); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here 275 | remover.Run(); | ~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' 59 | for (auto it = g_.SmartEdgeBegin(priority, conjugate_symmetry_); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 38 | return erroneous_edge_remover.Run(omnigraph::LengthComparator(g), | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | omnigraph::LengthUpperBound(g, max_length)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' 56 | return RemoveErroneousEdgesInLengthOrder(g, condition, max_length, removal_handler); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here 222 | while(debruijn::simplification::TopologyRemoveErroneousEdges(g, tec_config, 0)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here 29 | bool Load(const std::string &basename, Graph &graph) override { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here 42 | bool BinRead(std::istream &is, Graph &graph) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here 46 | void LoadImpl(BinIStream &str, Graph &graph) override { | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 83 | RemoveFromBorder(v); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 504 | component_.MakeInner(v); | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' 667 | if (component_searcher.FindComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: 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::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' 720 | [&](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&, __cxx11::basic_string, allocator >&}]' 119 | ::new((void*)__p) _Tp(std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/alloc_traits.h:694:19: [ 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::__cxx11::basic_string, 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&, 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::__cxx11::basic_string, std::allocator >&}; _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::__cxx11::basic_string, std::allocator >&}; _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&, __cxx11::basic_string, allocator >&}; 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-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: 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 >&)>]' 430 | return std::make_shared>(g, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 432 | info.chunk_cnt(), | ~~~~~~~~~~~~~~~~~ 433 | flanking_cov, | ~~~~~~~~~~~~~ 434 | rcc_config.coverage_gap, | ~~~~~~~~~~~~~~~~~~~~~~~~ 435 | size_t(double(info.read_length()) * rcc_config.length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 436 | size_t(double(info.read_length()) * rcc_config.tip_allowing_length_coeff), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 437 | connecting_path_length_bound, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 | max_coverage, | ~~~~~~~~~~~~~ 439 | removal_handler, rcc_config.vertex_count_limit, pics_dir); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:312:83: required from here 312 | auto algo = debruijn::simplification::RelativeCoverageComponentRemoverInstance(graph, flanking_cov, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 313 | standard_rcc_config(), | ~~~~~~~~~~~~~~~~~~~~~~ 314 | standard_simplif_relevant_info()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] 53 | size_t cnt = border_.erase(v); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 720 | auto interacting_edges = RetainIndependentBulges(bulges); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here 677 | size_t Run(bool force_primary_launch, double /*iter_run_progress*/) override { | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' 377 | for (; !it_.IsEnd(); ++it_) { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here 353 | size_t Run(bool force_primary_launch = false, | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:17: /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:100:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' 100 | Range r = NeighbourDistanceRange(v); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:990:43: 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]' 990 | dominated_set_finder.FillDominated(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1059:41: required from 'bool omnigraph::complex_br::CandidateFinder::Check(VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1059 | LocalizedComponentFinder comp_finder(g, max_length_, | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1057:10: required from here 1057 | bool Check(VertexId v) const override { | ^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:43:51: warning: unused parameter 'dominated_only' [-Wunused-parameter] 43 | Range NeighbourDistanceRange(VertexId v, bool dominated_only = true) const { | ~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 813 | if (!SplitComponent()) { | ^~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1121 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: 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]' 1149 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1195 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here 1189 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:777:26: warning: variable 'inner_v' set but not used [-Wunused-but-set-variable] 777 | VertexId inner_v = g_.EdgeEnd(split_res.first); | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:824:29: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 824 | EdgeId target = CorrespondingTreeEdge(*it); | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1121 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: 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]' 1149 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1195 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here 1189 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' 506 | queue_.pop(); | ~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' 251 | ++inner_it_; | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:822:43: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' 822 | gc.e_end()); !it.IsEnd(); ++it) { | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1121:44: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::ProcessComponent(omnigraph::complex_br::LocalizedComponent&, size_t) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 1121 | if (!projector.ProjectComponent()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1149:17: 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]' 1149 | if (ProcessComponent(component, candidate_cnt)) { | ^~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1195:13: required from 'bool omnigraph::complex_br::ComplexBulgeRemover::Process(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' 1195 | if (InnerProcess(v, vertices_to_post_process)) { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here 1189 | bool Process(VertexId v) override { | ^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here 309 | void HandleDelete(VertexId v) override { | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] 309 | void HandleDelete(VertexId v) override { | ~~~~~~~~~^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleMerge(const std::vector&, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:320:10: required from here 320 | void HandleMerge(const std::vector &old_edges, EdgeId /*new_edge*/) override { | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:322:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 322 | for (EdgeId e : old_edges) { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:18: required from here 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:476:71: warning: unused parameter 'edge2' [-Wunused-parameter] 476 | virtual void HandleGlue(EdgeId /*new_edge*/, EdgeId edge1, EdgeId edge2) { | ~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/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-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:241:18: required from here 241 | virtual void HandleSplit(EdgeId old_edge, EdgeId new_edge_1, EdgeId /*new_edge_2*/) { | ^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [408]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 408 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [408]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 408 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/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-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/14/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ [100%] Linking CXX executable ../../bin/debruijn_test cd /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -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/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 ../../ext/teamcity_gtest/libteamcity_gtest.a ../../lib/libgtest.a ../../common/paired_info/libpaired_info.a 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make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make -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-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 2%] Built target edlib [ 4%] Built target format [ 7%] Built target mimalloc-obj [ 9%] Built target gqf [ 12%] Built target version make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 12%] Built target gtest make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 12%] Built target coverage_model [ 12%] Built target binary_io [ 12%] Built target paired_info make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" [ 31%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target llvm-support make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target teamcity_gtest [ 56%] Built target sequence [ 58%] Built target utils make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" [ 65%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 73%] Built target assembly_graph [ 75%] Built target input make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 80%] Built target modules [ 90%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/pipeline/CMakeFiles/pipeline.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/stages/CMakeFiles/stages.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/CMakeFiles/common_modules.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/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-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test/CMakeFiles/include_test.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/quality_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/nucl_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:7: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:156:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:68: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:155:12: note: 's1$_M_elems$' was declared here 155 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, inlined from 'virtual void Seq_TestFirstLast_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:159:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:68: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_TestFirstLast_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:158:12: note: 's2$_M_elems$' was declared here 158 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:27:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftLeft_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:26:13: note: 's$_M_elems$' was declared here 26 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:40:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:341:42: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 341 | res.data_[i] = (res.data_[i] << 2) | rm; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ShiftRight_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:39:13: note: 's$_M_elems$' was declared here 39 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:384:37, inlined from 'virtual void Seq_Str_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:54:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Str_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:53:13: note: 's$_M_elems$' was declared here 53 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:199:35, inlined from 'virtual void Seq_HeadAndTail_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:61:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_HeadAndTail_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:60:13: note: 's$_M_elems$' was declared here 60 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:240:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:137:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:357:40: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 357 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:136:13: note: 's$_M_elems$' was declared here 136 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:240:20, inlined from 'virtual void Seq_ReverseComplement_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:141:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:357:40: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 357 | (data_[i >> TNuclBits] & ~((T) 3 << ((i & (TNucl - 1)) << 1))) | ((T) c << ((i & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_ReverseComplement_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:140:12: note: 's3$_M_elems$' was declared here 140 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:199:35, inlined from 'virtual void Seq_FromBiggerSeq_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:67:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_FromBiggerSeq_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:66:13: note: 's$_M_elems$' was declared here 66 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:199:35, 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:444:16, inlined from 'virtual void Seq_End_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:115:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_End_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:114:12: note: 's1$_M_elems$' was declared here 114 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:199:35, 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:438:16, inlined from 'virtual void Seq_Start_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:120:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Start_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:119:12: note: 's1$_M_elems$' was declared here 119 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:79:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:287:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 287 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:78:16: note: 's$_M_elems$' was declared here 78 | Seq<4> s("ACGT"); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include/gtest/gtest.h:387, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:83:38: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 83 | EXPECT_EQ("ACGTC", s.pushBack('C').str()); | ~~~~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:82:31: note: 's$_M_elems$' was declared here 82 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:87:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:287:59: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 287 | s.data_[s.DataSize - 1] = s.data_[s.DataSize - 1] | ((T) c << ((size_ & (TNucl - 1)) << 1)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_PushBack_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:86:16: note: 's$_M_elems$' was declared here 86 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:151:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_2_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:150:13: note: 's$_M_elems$' was declared here 150 | 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-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:146:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:265:54: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 265 | data[DataSize - 1] = (data[DataSize - 1] >> 2) | ((T) c << lastnuclshift_); | ~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp: In member function 'virtual void Seq_Test16_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:145:13: note: 's$_M_elems$' was declared here 145 | Seq<16> s("AAAAAAAAAAAAAAAA"); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/rtseq.hpp:25, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:7: 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:384:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:336:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:328:12: note: 's$_M_elems$' was declared here 328 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:384:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:337:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's1$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:329:13: note: 's1$_M_elems$' was declared here 329 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:384:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:338:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's2$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:330:13: note: 's2$_M_elems$' was declared here 330 | 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-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:384:37, inlined from 'virtual void RtSeq_FromSeq_Test::TestBody()' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:339:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:227:39: warning: 's3$_M_elems$' may be used uninitialized [-Wmaybe-uninitialized] 227 | return (data_[i >> TNuclBits] >> ((i & (TNucl - 1)) << 1)) & 3; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp: In member function 'virtual void RtSeq_FromSeq_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp:331:13: note: 's3$_M_elems$' was declared here 331 | Seq<32> s3("ACGTACGTACACGTACGTACACGTACGTACAC"); | ^~ [100%] Linking CXX executable ../../bin/include_test cd /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -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 ../../lib/libgtest.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-19/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/llvm-19/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target include_test make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_auto_test -O--sourcedirectory=assembler/src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu 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 test 1 Start 1: include_test 1: Test command: /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/bin/include_test 1: Working Directory: /build/reproducible-path/spades-3.15.5+dfsg/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-3.15.5+dfsg/obj-x86_64-linux-gnu/bin/debruijn_test 2: Working Directory: /build/reproducible-path/spades-3.15.5+dfsg/assembler/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. (1 ms total) 1: [ PASSED ] 58 tests. 2: Running main() from gtest_main.cpp 2: [==========] Running 98 tests from 10 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator 2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge 2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (1 ms) 2: [----------] 6 tests from GraphCore (1 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: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.001 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 1/2 Test #1: include_test ..................... Passed 0.03 sec 2: [ OK ] PairedInfo.RandomSymmetry (71 ms) 2: [----------] 13 tests from PairedInfo (72 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: 0:00:00.073 1M / 9M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.082 1M / 9M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.083 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp 2: 0:00:00.083 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.086 1M / 13M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (28 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.102 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.102 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.102 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.102 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.102 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.103 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (2 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.103 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.103 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.103 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.103 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.103 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.103 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.104 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.104 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.104 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.104 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.150 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (77 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.180 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.181 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.181 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.181 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.223 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (71 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.251 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.254 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.254 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.254 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.294 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (72 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.323 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.323 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.323 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.323 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.361 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.362 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology 2: 0:00:00.376 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (80 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.403 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.403 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.403 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp 2: 0:00:00.403 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.436 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.437 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (89 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.493 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.493 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.493 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp 2: 0:00:00.493 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.493 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.494 1M / 61M INFO General (simplification_test.cpp : 276) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (4 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.496 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.496 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.496 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.496 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.496 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.544 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.545 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) 2: 0:00:00.592 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.691 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:00.692 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.742 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.742 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (401 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.898 1M / 63M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.898 1M / 63M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.898 1M / 63M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.898 1M / 63M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp 2: 0:00:00.898 1M / 63M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:01.108 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:01.110 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) 2: 0:00:01.144 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.192 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). 2: 0:00:01.192 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.240 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:01.313 1161M / 1161M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: [ OK ] Simplification.BigComplexBulge (469 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:01.366 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.366 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.366 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.366 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp 2: 0:00:01.366 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:01.368 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:01.368 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) 2: 0:00:01.374 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.422 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). 2: 0:00:01.422 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.440 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:01.440 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:01.440 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (133 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:01.500 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.500 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.500 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.500 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:01.500 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:01.536 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:01.537 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) 2: 0:00:01.585 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.684 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). 2: 0:00:01.684 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.734 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:01.734 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:01.734 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (283 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:01.783 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.783 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.783 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.783 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp 2: 0:00:01.783 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:01.783 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.783 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) 2: 0:00:01.784 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.786 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). 2: 0:00:01.786 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.787 3M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:01.788 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:01.788 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (18 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:01.800 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.801 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.801 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.801 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:01.801 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:01.801 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.801 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) 2: 0:00:01.801 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.802 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). 2: 0:00:01.802 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.802 1M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:01.802 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:01.802 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (4 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:01.804 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.804 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.804 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.804 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp 2: 0:00:01.804 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:01.804 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.805 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) 2: 0:00:01.806 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.813 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). 2: 0:00:01.813 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.816 4M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:01.816 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:01.816 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (33 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:01.837 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.837 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.837 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:01.837 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:01.837 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:01.837 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:01.837 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) 2: 0:00:01.838 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.838 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). 2: 0:00:01.838 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:01.838 2M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:01.838 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: [ OK ] Simplification.CompressorTest (2 ms) 2: [----------] 17 tests from Simplification (1766 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:01.839 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.839 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.839 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:01.839 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.839 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:01.839 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.839 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:01.850 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads 2: 0:00:01.850 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:01.852 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. 2: 0:00:01.852 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:01.852 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.852 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:01.852 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.852 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:01.860 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. 2: 0:00:01.861 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:01.863 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. 2: 0:00:01.863 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.863 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). 2: 0:00:01.863 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:01.937 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:01.938 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.938 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:01.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:01.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:01.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:01.938 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (104 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:01.943 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.943 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.943 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:01.943 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.944 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:01.944 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.944 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:01.962 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:01.962 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:01.964 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. 2: 0:00:01.964 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:01.964 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:01.964 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:01.964 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:01.964 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:01.977 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. 2: 0:00:01.977 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:01.980 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. 2: 0:00:01.980 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:01.981 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). 2: 0:00:01.981 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:01.982 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:01.982 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:01.983 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:01.983 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:01.983 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:01.983 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:01.983 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:01.983 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (56 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:02.000 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.000 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.000 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.000 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.000 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.000 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.000 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.011 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:02.011 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.014 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:02.014 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.014 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.014 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.014 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.014 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.027 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. 2: 0:00:02.027 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.029 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:02.029 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.030 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:02.030 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.031 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.031 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.031 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.032 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.032 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:02.032 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.032 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create 2: 0:00:02.032 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (34 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:02.034 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.034 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.034 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.034 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.043 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.043 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.043 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.052 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:02.052 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.055 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:02.057 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.057 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.057 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.057 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.057 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.066 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. 2: 0:00:02.066 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.070 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:02.070 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.071 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). 2: 0:00:02.071 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.073 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.074 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.074 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.074 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.074 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:02.074 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.074 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.074 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create 2: 0:00:02.074 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.075 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.075 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.075 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create 2: 0:00:02.075 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (43 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:02.076 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.076 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.076 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.076 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.076 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.076 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.076 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.086 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:02.086 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.092 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:02.092 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.092 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.092 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.092 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.092 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.102 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. 2: 0:00:02.102 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.108 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:02.108 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.109 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:02.109 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.112 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.112 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.112 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.113 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.113 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:02.113 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.113 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:02.113 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (39 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:02.116 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.116 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.116 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.116 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.116 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.116 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.116 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.126 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:02.126 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.129 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.130 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.130 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.130 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.130 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.130 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.139 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:02.139 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.144 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.144 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.145 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:02.145 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.147 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.147 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.147 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.147 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.147 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:02.148 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.148 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:02.148 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (33 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:02.149 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.149 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.149 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:02.149 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.149 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.150 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.150 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.150 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.161 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:02.161 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.164 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.164 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.164 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.164 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.164 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.164 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.179 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:02.179 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.181 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.181 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.183 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:02.183 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.185 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.185 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.186 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.186 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.186 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:02.186 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.186 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:02.186 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:02.186 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:02.186 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) 2: 0:00:02.186 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.186 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:02.186 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (39 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:02.187 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.187 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.187 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:02.187 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:02.187 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.187 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.188 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.188 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.201 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:02.201 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.205 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.205 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.205 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.206 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.206 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.206 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.216 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:02.217 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.221 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:02.221 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.222 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:02.222 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.225 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.225 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.225 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.226 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.226 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:02.226 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.226 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:02.226 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:02.227 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:02.228 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) 2: 0:00:02.228 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.228 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:02.228 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (43 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:02.230 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.230 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.230 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:02.230 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 2: 0:00:02.230 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.230 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.230 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.230 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.242 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:02.243 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.247 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. 2: 0:00:02.247 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:02.247 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:02.248 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:02.248 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:02.248 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:02.257 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. 2: 0:00:02.257 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:02.261 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. 2: 0:00:02.261 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.262 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). 2: 0:00:02.262 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:02.263 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:02.264 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:02.264 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:02.264 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:02.264 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:02.264 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:02.264 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 2: 0:00:02.264 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:02.264 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:02.264 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) 2: 0:00:02.264 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.264 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). 2: 0:00:02.264 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:02.264 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index 2: 0:00:02.264 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:02.265 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). 2: 0:00:02.265 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:02.265 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM 2: 0:00:02.267 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:02.267 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done 2: 0:00:02.291 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (76 ms) 2: [----------] 9 tests from GraphConstruction (467 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order 2: 0:00:02.306 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.306 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.375 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.375 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (70 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (9 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [----------] 3 tests from Io (79 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:02.385 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.386 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove 2: 0:00:02.386 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.386 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.386 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.387 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.387 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate 2: 0:00:02.388 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.388 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch 2: 0:00:02.388 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.388 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.388 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector 2: 0:00:02.389 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.389 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) 2: [----------] 8 tests from PathExtend (4 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:02.389 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.389 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.389 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicNoDiff (1 ms) 2: [ RUN ] OverlapRemoval.BasicDiff 2: 0:00:02.390 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.390 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges 2: 0:00:02.390 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.390 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:02.390 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:02.391 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:02.391 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (1 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:02.391 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.391 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.391 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.391 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.400 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.401 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (10 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:02.401 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.401 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.401 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.401 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.408 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.408 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:02.408 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.408 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.408 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.408 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.415 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.415 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.415 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:02.416 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.416 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.416 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.416 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.423 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.423 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (8 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:02.423 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.423 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.423 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.423 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.430 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.430 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.430 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:02.430 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.430 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.430 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.430 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.437 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.437 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.437 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:02.437 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.437 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.437 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.437 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.444 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.444 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.444 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (7 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:02.444 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.444 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.444 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.444 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.451 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.452 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.452 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (8 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:02.452 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.452 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.452 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.452 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.459 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (7 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:02.459 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.459 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.459 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.459 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.466 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:02.466 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.466 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.466 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.466 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.473 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:02.473 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.473 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.473 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.473 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.480 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:02.480 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.480 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.480 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.480 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.487 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (7 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:02.487 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.487 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.487 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.487 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.494 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (7 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:02.494 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.494 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.494 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.494 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.504 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.504 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.504 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (10 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:02.504 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.504 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.504 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.504 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.511 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.511 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.511 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (7 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:02.511 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.512 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.512 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.512 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.521 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.521 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.521 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (10 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:02.522 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.522 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.522 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.522 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.531 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.531 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.531 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (10 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:02.531 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.531 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.531 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.531 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.538 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.539 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.539 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (8 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:02.539 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.539 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.539 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.539 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.546 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.546 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:02.546 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (7 ms) 2: [----------] 23 tests from OverlapRemoval (157 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:02.546 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:02.546 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 2: 0:00:02.546 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:02.546 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:02.546 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:02.546 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:02.546 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:02.553 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:02.565 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (696 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:03.242 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:03.243 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:03.243 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:03.243 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:03.250 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (9 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:03.251 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:03.251 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:03.251 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:03.251 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:03.258 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (7 ms) 2: [----------] 5 tests from GraphAligner (712 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 98 tests from 10 test suites ran. (3258 ms total) 2: [ PASSED ] 98 tests. 2/2 Test #2: debruijn_test .................... Passed 3.27 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 3.28 sec make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=assembler/src -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/metaspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/plasmidspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/rnaspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/metaviralspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/metaplasmidspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/rnaviralspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/coronaspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/truspades.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades_init.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/VERSION -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.gff -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/genes_1K.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: 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/build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/rnaspades_manual.html -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/LICENSE -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/GPLv2.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-core -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/hmm_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/isolate_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/tsa.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaviral_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/simplification.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/pe_params.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info -- 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/build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/corrector/corrector.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-truseq-scfcorrection -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-kmercount -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-read-filter -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-kmer-estimating -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-convert-bin-to-fasta -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-gbuilder -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-gmapper -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spaligner -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spaligner/spaligner_config.yaml -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/spades-gsimplifier -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/cds-subgraphs -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/cds-mapping-stats -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/bin/mag-improve -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/run_contig_breaker.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/commands_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/support.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_storage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline/options_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/compress_all.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/breaking_scaffolds_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/correction_iteration_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/postprocessing_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/plasmid_glue.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/before_start_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/check_test_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/correction_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/terminating_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/postprocessing_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/pipeline.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/error_correction_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/preprocess_reads_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/breaking_scaffolds_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_postprocessing.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/string_dist_utils.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/moleculo_filter_contigs.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/launch_options.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/break_by_coverage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/generate_quality.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/reference_construction.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/id_generation.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//truspades/barcode_extraction.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/parallel_launcher.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/sam_parser.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/SeqIO.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_save_yaml.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executor_local.py make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' # 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-3.15.5+dfsg' dh_install -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installdocs -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' LANG="C" LANGUAGE="en_US:en" LC_ALL=C.UTF-8 lynx -dump assembler/changelog.html > changelog dh_installchangelogs changelog rm changelog make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg' mkdir -p /build/reproducible-path/spades-3.15.5+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/reproducible-path/spades-3.15.5+dfsg/debian/man_src/*.adoc cp /build/reproducible-path/spades-3.15.5+dfsg/debian/man_src/*.? /build/reproducible-path/spades-3.15.5+dfsg/debian/man dh_installman make[1]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg' dh_python3 -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installsystemduser -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_perl -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_link -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_strip_nondeterminism -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_compress -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_fixperms -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_missing -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_dwz -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_strip -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_makeshlibs -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_shlibdeps -a -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installdeb -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_gencontrol -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_md5sums -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_builddeb -O--sourcedirectory=assembler/src -O--buildsystem=cmake dpkg-deb: building package 'spades' in '../spades_3.15.5+dfsg-8_amd64.deb'. dpkg-deb: building package 'spades-dbgsym' in '../spades-dbgsym_3.15.5+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_3.15.5+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_3.15.5+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1319961/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1319961 and its subdirectories I: Current time: Sun Dec 15 10:43:06 +14 2024 I: pbuilder-time-stamp: 1734208986