I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 13 23:41:07 +14 2025 I: pbuilder-time-stamp: 1749807667 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-7.dsc] I: copying [./spades_3.15.5+dfsg.orig.tar.xz] I: copying [./spades_3.15.5+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Feb 2 09:34:41 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./spades_3.15.5+dfsg-7.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-7.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4087328/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 13 09:41 /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/4087328/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4087328/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=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=9c65ed1f2ff24364bb20b880791b8f5d 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=4087328 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.ku2pVp5M/pbuilderrc_ORUa --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.ku2pVp5M/b2 --logfile b2/build.log spades_3.15.5+dfsg-7.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 11 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4087328/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 ... 19700 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-16{a} clang-format{a} clang-format-16{a} clang-tidy{a} clang-tidy-16{a} clang-tools{a} clang-tools-16{a} cmake{a} cmake-data{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} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libbsd0{a} libbwa-dev{a} libbz2-dev{a} libc++-16-dev{a} libc++-dev{a} libc++1-16t64{a} libc++abi1-16t64{a} libclang-common-16-dev{a} libclang-cpp16t64{a} libclang1-16t64{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} libexpat1{a} libffi-dev{a} libfile-stripnondeterminism-perl{a} libgc1{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libllvm16t64{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libobjc-13-dev{a} libobjc4{a} libpfm4{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhash0{a} librtmp1{a} libruby{a} libruby3.1t64{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libunwind-16-dev{a} libunwind-16t64{a} libuv1t64{a} libxml2{a} libxml2-dev{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzstd-dev{a} llvm{a} llvm-16{a} llvm-16-dev{a} llvm-16-linker-tools{a} llvm-16-runtime{a} llvm-16-tools{a} llvm-dev{a} llvm-runtime{a} lynx{a} lynx-common{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-distutils{a} python3-joblib{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-pygments{a} python3-setuptools{a} python3-yaml{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-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-16-dev libgpm2 libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules mailcap psmisc publicsuffix python3-numpy python3-psutil python3-pytest python3-simplejson systemd zip 0 packages upgraded, 158 newly installed, 0 to remove and 0 not upgraded. Need to get 203 MB of archives. After unpacking 1104 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 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 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 31 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.20-1 [212 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.20-1 [87.7 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.17-7+b3 [212 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libllvm16t64 amd64 1:16.0.6-27 [23.1 MB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libclang-cpp16t64 amd64 1:16.0.6-27 [11.5 MB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libgc1 amd64 1:8.2.6-1 [244 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libobjc4 amd64 14-20240429-1 [42.4 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libobjc-13-dev amd64 13.2.0-24 [170 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libclang-common-16-dev amd64 1:16.0.6-27 [656 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 llvm-16-linker-tools amd64 1:16.0.6-27 [1242 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libclang1-16t64 amd64 1:16.0.6-27 [6581 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 clang-16 amd64 1:16.0.6-27 [111 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 clang-format-16 amd64 1:16.0.6-27 [82.8 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 clang-format amd64 1:16.0-58.1 [5552 B] Get: 67 http://deb.debian.org/debian unstable/main amd64 clang-tools-16 amd64 1:16.0.6-27 [7798 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 clang-tidy-16 amd64 1:16.0.6-27 [4150 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 clang-tidy amd64 1:16.0-58.1 [5324 B] Get: 71 http://deb.debian.org/debian unstable/main amd64 clang-tools amd64 1:16.0-58.1 [5336 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 78 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 100 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libbam-dev amd64 0.1.19+dfsg-6 [118 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [159 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libbamtools-dev amd64 2.5.2+dfsg-5 [221 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.17-7+b3 [156 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libunwind-16t64 amd64 1:16.0.6-27 [55.8 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libc++abi1-16t64 amd64 1:16.0.6-27 [94.0 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libc++1-16t64 amd64 1:16.0.6-27 [296 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libunwind-16-dev amd64 1:16.0.6-27 [74.3 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libc++-16-dev amd64 1:16.0.6-27 [1062 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libc++-dev amd64 1:16.0-58.1 [5248 B] Get: 124 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-5 [538 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5-2 [349 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-5+b2 [174 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libnlopt-dev amd64 2.7.1-5+b2 [46.8 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx0 amd64 2.7.1-5+b2 [201 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libnlopt-cxx-dev amd64 2.7.1-5+b2 [13.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git32-g0d4ed0e-1 [341 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libssw-dev amd64 1.1-14+b1 [24.0 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.3+b3 [787 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libz3-dev amd64 4.8.12-3.1+b2 [90.9 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 llvm-16-runtime amd64 1:16.0.6-27 [519 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 llvm-runtime amd64 1:16.0-58.1 [5104 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 llvm-16 amd64 1:16.0.6-27 [21.1 MB] Get: 149 http://deb.debian.org/debian unstable/main amd64 llvm amd64 1:16.0-58.1 [7488 B] Get: 150 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.17.2+dfsg-1 [818 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 llvm-16-tools amd64 1:16.0.6-27 [479 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 llvm-16-dev amd64 1:16.0.6-27 [37.7 MB] Get: 153 http://deb.debian.org/debian unstable/main amd64 llvm-dev amd64 1:16.0-58.1 [5352 B] Get: 154 http://deb.debian.org/debian unstable/main amd64 lynx-common all 2.9.1-1 [1193 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 lynx amd64 2.9.1-1 [638 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Fetched 203 MB in 2s (98.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19700 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20016 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21008 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../007-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../008-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../009-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../010-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../011-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../012-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../013-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../015-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../016-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../017-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../018-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../019-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../020-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../021-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../022-ruby-sdbm_1.0.0-5+b4_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b4) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../023-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../024-libedit2_3.1-20230828-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../025-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../026-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../027-libruby3.1t64_3.1.2-8.3_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../028-ruby3.1_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../029-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../030-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../031-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../032-ruby-asciidoctor_2.0.20-1_all.deb ... Unpacking ruby-asciidoctor (2.0.20-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../033-asciidoctor_2.0.20-1_all.deb ... Unpacking asciidoctor (2.0.20-1) ... Selecting previously unselected package m4. Preparing to unpack .../034-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../035-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../036-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../037-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../038-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package bwa. Preparing to unpack .../039-bwa_0.7.17-7+b3_amd64.deb ... Unpacking bwa (0.7.17-7+b3) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../040-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../041-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../042-libz3-4_4.8.12-3.1+b2_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1+b2) ... Selecting previously unselected package libllvm16t64:amd64. Preparing to unpack .../043-libllvm16t64_1%3a16.0.6-27_amd64.deb ... Unpacking libllvm16t64:amd64 (1:16.0.6-27) ... Selecting previously unselected package libclang-cpp16t64. Preparing to unpack .../044-libclang-cpp16t64_1%3a16.0.6-27_amd64.deb ... Unpacking libclang-cpp16t64 (1:16.0.6-27) ... 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Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jun 13 09:41:57 UTC 2025. Universal Time is now: Fri Jun 13 09:41:57 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libpfm4:amd64 (4.13.0+git32-g0d4ed0e-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up autopoint (0.21-14) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-4+b1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up lynx-common (2.9.1-1) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-5) ... Setting up libgc1:amd64 (1:8.2.6-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7+b3) ... 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Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... 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 (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libz3-dev:amd64 (4.8.12-3.1+b2) ... Setting up libncurses-dev:amd64 (6.5-2) ... Setting up gettext (0.21-14+b1) ... Setting up libssw-dev:amd64 (1.1-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libobjc4:amd64 (14-20240429-1) ... Setting up libc++abi1-16t64:amd64 (1:16.0.6-27) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libllvm16t64:amd64 (1:16.0.6-27) ... 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 (2.7.1-5+b2) ... Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libbam-dev (0.1.19+dfsg-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up lynx (2.9.1-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libobjc-13-dev:amd64 (13.2.0-24) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libc++1-16t64:amd64 (1:16.0.6-27) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up llvm-16-runtime (1:16.0.6-27) ... 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Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up asciidoctor (2.0.20-1) ... Processing triggers for libc-bin (2.38-8) ... 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/4087328/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/4087328/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-7_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.5+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 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 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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. -- 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 < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -- Performing Test Terminfo_LINKABLE -- Performing Test Terminfo_LINKABLE - Success -- Found Terminfo: /usr/lib/x86_64-linux-gnu/libtinfo.so -- 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 "8.7.1") -- 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 < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. 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 < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. 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 "3.11.9") CMake Deprecation Warning at projects/mts/CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done (14.1s) -- Generating done (0.5s) 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 -j42 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks 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 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/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 make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o [ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 1%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o [ 1%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 5%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 5%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.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/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 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/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 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 [ 1%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 1%] 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/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 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 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 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_MALLOC_OVERRIDE_GLIBC -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -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++17 -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -Wno-invalid-memory-model -ftls-model=initial-exec -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-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 make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build 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/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamAlignment.cpp make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamMultiReader.cpp 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 make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build 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 make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build 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 make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/build 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 make[4]: Entering 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 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 make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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 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 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/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 make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 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 make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/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 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 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 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 5%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o [ 5%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o [ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 5%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 6%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wall -Wextra -pedantic -Wno-deprecated -O2 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/cppformat/format.cc 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/AffineAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp [ 6%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o [ 6%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c [ 6%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-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/edlib/CMakeFiles/edlib.dir/edlib.cpp.o -MF CMakeFiles/edlib.dir/edlib.cpp.o.d -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/edlib/edlib.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o -MF CMakeFiles/llvm-support.dir/APFloat.cpp.o.d -o CMakeFiles/llvm-support.dir/APFloat.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/APFloat.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-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.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest-all.cc [ 6%] 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/gfa1 && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -MF CMakeFiles/gfa1.dir/gfa.c.o.d -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/gfa1/gfa.c 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 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 [ 6%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.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/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 /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 8%] Linking CXX static library libversion.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 /usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o /usr/bin/ranlib libversion.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/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 { | ^~~~~~~~~~~~ [ 8%] Built target version 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 { | ^~~~~~~~~ [ 9%] 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 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); | ^~~~~~~~~~~ [ 9%] 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 [ 9%] 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 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 { | ^~~~~~~~~ [ 10%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o [ 10%] 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp [ 10%] Building CXX object ext/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 [ 10%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o [ 10%] 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/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 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/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 [ 11%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o [ 11%] 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/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 [ 11%] 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/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 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 [ 11%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o [ 12%] 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/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 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 [ 12%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o [ 12%] 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/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/Coverage.cpp.o -MF CMakeFiles/ConsensusCore.dir/Coverage.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 [ 12%] 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': 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); | ^~~~~~~~~~~~~~~ /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/block.c:4: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/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/bgzf.c:32: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' 578 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 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); | ^~~~~~~~ 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); | ^~~~~~~~~~~~~~~ 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:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined 8 | safe_mutex_unlock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined 5 | safe_mutex_lock(pthread_mutex_t *mutex); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ 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); | ^~~~~~~~~~~ [ 12%] 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 [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o [ 12%] Linking C static library libgqf.a [ 12%] 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/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/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 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 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 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 [ 12%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.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/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp [ 12%] 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 /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o [ 12%] 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 [ 13%] 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 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-isystem /build/reproducible-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 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 15%] 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 [ 15%] Built target gqf [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 15%] 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 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 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); | ^~~~~~~~~~~ [ 15%] 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 [ 16%] 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 [ 16%] 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 [ 16%] 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 [ 16%] 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 [ 16%] 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 [ 16%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.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/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 [ 16%] 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 [ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o -MF CMakeFiles/easel.dir/esl_exponential.c.o.d -o CMakeFiles/easel.dir/esl_exponential.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_exponential.c [ 16%] 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 [ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:14: note: did you mean to dereference the pointer? 278 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ [ 17%] Building 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 [ 17%] Linking CXX static library libgetopt_pp.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake [ 18%] 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o [ 19%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp /usr/bin/ranlib libgetopt_pp.a [ 19%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o [ 19%] 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/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 [ 19%] 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 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 [ 19%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o [ 19%] 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 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/ranlib libgfa1.a [ 19%] 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 [ 19%] Built target getopt_pp [ 19%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 19%] 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 [ 19%] Built target gfa1 [ 20%] 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 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-fstack-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 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' [ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c [ 20%] Building 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 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-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 [ 20%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp [ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c [ 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 [ 23%] 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o [ 23%] 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 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-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 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' [ 24%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o cd 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-o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp [ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c [ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/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 [ 24%] 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 [ 25%] 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ [ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o [ 26%] 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/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 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 [ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd 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-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 [ 26%] 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/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp [ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp /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_ ? | ^~~~~~~ [ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp [ 27%] 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 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:207:19: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/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 /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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] /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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:219:41: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:253:22: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::EdgesPositionHandler]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:256:45: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] [ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp [ 27%] 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 [ 27%] 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 [ 27%] 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 [ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp [ 27%] 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 [ 27%] 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 [ 29%] 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 [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o [ 29%] 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/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 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 [ 29%] 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 -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp [ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp [ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o [ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 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 [ 31%] 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 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/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/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 31%] 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 [ 31%] 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 [ 31%] 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 [ 31%] 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 [ 31%] 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 [ 31%] 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 [ 31%] 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 [ 32%] Linking CXX static library libformat.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] 94 | mi = ::mallinfo(); | ~~~~~~~~~~^~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: /usr/include/malloc.h:114:24: note: declared here 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; | ^~~~~~~~ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o [ 32%] Building 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 [ 33%] 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 [ 34%] 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 /usr/bin/ranlib libformat.a [ 34%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 34%] Built target format [ 34%] 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 file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 34%] Built target mimalloc-obj [ 34%] 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 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:109:33: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ [ 34%] 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 [ 34%] 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 [ 34%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c [ 36%] Linking CXX static library libBamTools.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake 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 [ 36%] 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 [ 36%] Linking CXX static library libsequence.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake /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 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=" cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 /usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o 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' [ 36%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o -MF CMakeFiles/utils.dir/memory_limit.cpp.o.d -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/memory_limit.cpp /usr/bin/ranlib libsequence.a [ 37%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o /usr/bin/ranlib libBamTools.a 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 [ 37%] 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 [ 37%] 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 37%] Built target sequence [ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c [ 37%] Building CXX object common/utils/CMakeFiles/utils.dir/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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 37%] Built target BamTools [ 37%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c [ 38%] 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 [ 38%] 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 [ 38%] 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 [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend 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 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/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=" [ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_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 make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 39%] 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 [ 39%] 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 [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kstring.c [ 39%] 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 [ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 40%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c [ 40%] 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:178:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 41%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o [ 41%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/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 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 41%] 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 [ 43%] 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 [ 43%] 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 [ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o [ 44%] 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/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c 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 [ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 [ 44%] 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 /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 44%] 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 45%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o [ 44%] 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 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 [ 45%] 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 [ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c [ 45%] 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 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 45%] 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 [ 45%] 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 [ 45%] 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 [ 46%] 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 [ 46%] 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 /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 46%] 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 [ 46%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c [ 46%] Building C object ext/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 [ 47%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-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_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 [ 47%] 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 [ 47%] 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 [ 47%] 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 [ 47%] 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 [ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c [ 48%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-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 [ 48%] 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 /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 50%] Linking CXX static library libgraphio.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o /usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 50%] Built target graphio [ 50%] Linking CXX static library libsamtools.a cd 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/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 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-c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_stotrace.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.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 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ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.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 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-I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 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 [ 56%] Built target coverage_model [ 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 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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 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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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxchk.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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/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 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -MF CMakeFiles/hmmer.dir/src/p7_spensemble.c.o.d -o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_spensemble.c cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_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 [ 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 In file included from /usr/include/string.h:548, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:13: In function 'memset', inlined from 'destroy_worker' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:1119:5, inlined from 'update_workers' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:287:7: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_trace.c.o /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: note: in a call to built-in function '__builtin_memset' 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 [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_scoredata.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_scoredata.c.o -MF CMakeFiles/hmmer.dir/src/p7_scoredata.c.o.d -o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_scoredata.c [ 61%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_alphabet.c.o [ 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 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/impl_sse/decoding.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/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 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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/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 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/fm_sse.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c [ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/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 [ 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 [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/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/vitfilter.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c [ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 65%] Linking CXX static library libutils.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 65%] Built target utils In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:12: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 65%] Linking CXX static library libllvm-support.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" [ 65%] 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 /usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o /usr/bin/ranlib libllvm-support.a /usr/bin/ranlib libmapping_printer.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 65%] Built target mapping_printer make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 65%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o [ 66%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o [ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/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/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 68%] Linking C static library libhmmer.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/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 In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /usr/bin/ranlib libhmmer.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target hmmer make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o [ 68%] 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 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/index/edge_info_updater.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp: In instantiation of 'class debruijn_graph::EdgeInfo': /usr/include/c++/13/bits/stl_vector.h:1018:43: required from 'void std::vector<_Tp, _Alloc>::resize(size_type) [with _Tp = debruijn_graph::EdgeInfo; _Alloc = std::allocator >; size_type = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:163:21: required from 'void utils::PerfectHashMap::resize(size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; Container = std::vector, std::allocator > >; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:43:21: required from 'void utils::PerfectHashMapBuilder::BuildIndex(utils::PerfectHashMap&, const KMerStorage&, size_t) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = utils::InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:144:39: required from 'void utils::BuildIndex(PerfectHashMap&, const KMerStorage&, size_t) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfo; traits = kmers::kmer_index_traits >; StoringType = InvertableStoring; KMerStorage = debruijn_graph::GraphPositionFillingIndexBuilder >::KMerFullGraphStorage; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:249:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const debruijn_graph::Graph&) const [with Index = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:27:39: required from 'void debruijn_graph::EdgeIndexRefiller::Refill(EdgeIndex&, const debruijn_graph::Graph&) [with EdgeIndex = debruijn_graph::KmerFreeEdgeIndex; debruijn_graph::Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:31:64: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 20 | IdHolder edge_id_; | ^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /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; | ~~~~^ [ 68%] Linking CXX static library libpaired_info.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 /usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o [ 68%] Linking CXX static library libhmmercpp.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 /usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o /usr/bin/ranlib libpaired_info.a /usr/bin/ranlib libhmmercpp.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target hmmercpp [ 68%] Built target paired_info /build/reproducible-path/spades-3.15.5+dfsg/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::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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 68%] Linking CXX static library ../../../lib/libgtest.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" /usr/bin/ranlib ../../../lib/libgtest.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target gtest make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /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 [ 68%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o [ 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 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 In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 68%] Linking CXX static library ../../../lib/libgtest_main.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o /usr/bin/ranlib ../../../lib/libgtest_main.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target gtest_main 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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 68%] Linking CXX static library libteamcity_gtest.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 /usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o /usr/bin/ranlib libteamcity_gtest.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target teamcity_gtest In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 68%] Linking CXX static library libConsensusCore.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o /usr/bin/ranlib libConsensusCore.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 68%] Built target ConsensusCore make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o [ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/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 [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o [ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp [ 72%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp 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 [ 72%] Linking CXX static library libassembly_graph.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 /usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o /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()); | ^~~~ /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src 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libbinary_io.a [ 72%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o [ 73%] 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/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/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/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 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 [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o [ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.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 [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o [ 75%] 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 && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -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 [ 75%] 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 && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -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 [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o [ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o cd 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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 [ 76%] 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/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 [ 76%] 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/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 [ 76%] 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/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/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/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 [ 76%] 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/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 [ 77%] 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 && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -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/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 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 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 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 [ 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/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp 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 [ 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 [ 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 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' [ 79%] Built target binary_io make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o 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 [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/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/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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /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) | ~~~~~~~^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp: In instantiation of 'std::vector debruijn_graph::GetCommonPathsEnd(const Graph&, typename Graph::EdgeId, typename Graph::EdgeId, size_t, size_t, typename omnigraph::DijkstraHelper::BoundedDijkstra&) [with Graph = DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename omnigraph::DijkstraHelper::BoundedDijkstra = omnigraph::Dijkstra, omnigraph::BoundProcessChecker, omnigraph::BoundPutChecker, omnigraph::ForwardNeighbourIteratorFactory, long unsigned int>, long unsigned int>]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:103:64: required from 'std::vector > debruijn_graph::SplitPathConstructor::ConvertPIToSplitPaths(EdgeId, omnigraph::de::PairedInfoIndexT&, double, double) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId; omnigraph::de::PairedInfoIndexT = omnigraph::de::PairedIndex]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:230:55: required from 'size_t debruijn_graph::PairInfoImprover::FillMissing(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:102:37: required from 'void debruijn_graph::PairInfoImprover::CorrectPairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:93:9: required from 'void debruijn_graph::PairInfoImprover::ImprovePairedInfo(unsigned int) [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:165:31: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 28 | size_t min_dist, | ~~~~~~~^~~~~~~~ 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; | ^~~~~~~ [ 79%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp /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_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp [ 80%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 111 | if (iter->second < min_read_count_) { | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/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/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_utils.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /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_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ [ 81%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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/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, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:34:58: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/visualization/position_filler.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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/modules/chromosome_remover.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:34:13: note: in expansion of macro 'SET_PRIORITY' 34 | SET_PRIORITY(LibraryType::SangerReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:35:13: note: in expansion of macro 'SET_PRIORITY' 35 | SET_PRIORITY(LibraryType::PacBioReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:36:13: note: in expansion of macro 'SET_PRIORITY' 36 | SET_PRIORITY(LibraryType::NanoporeReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:37:13: note: in expansion of macro 'SET_PRIORITY' 37 | SET_PRIORITY(LibraryType::TrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:38:13: note: in expansion of macro 'SET_PRIORITY' 38 | SET_PRIORITY(LibraryType::SingleReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:39:13: note: in expansion of macro 'SET_PRIORITY' 39 | SET_PRIORITY(LibraryType::PairedEnd); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:40:13: note: in expansion of macro 'SET_PRIORITY' 40 | SET_PRIORITY(LibraryType::HQMatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:41:13: note: in expansion of macro 'SET_PRIORITY' 41 | SET_PRIORITY(LibraryType::MatePairs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:42:13: note: in expansion of macro 'SET_PRIORITY' 42 | SET_PRIORITY(LibraryType::TSLReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:43:13: note: in expansion of macro 'SET_PRIORITY' 43 | SET_PRIORITY(LibraryType::PathExtendContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:44:13: note: in expansion of macro 'SET_PRIORITY' 44 | SET_PRIORITY(LibraryType::UntrustedContigs); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:45:13: note: in expansion of macro 'SET_PRIORITY' 45 | SET_PRIORITY(LibraryType::FLRNAReads); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:33: note: here 28 | #define SET_PRIORITY(o) case o: --priority | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' 46 | SET_PRIORITY(LibraryType::AssemblyGraph); | ^~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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_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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/alloc_traits.h:39, from /usr/include/c++/13/ext/alloc_traits.h:34, from /usr/include/c++/13/bits/hashtable_policy.h:39, from /usr/include/c++/13/bits/hashtable.h:35, from /usr/include/c++/13/bits/unordered_map.h:33, from /usr/include/c++/13/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: 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/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/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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/streambuf:43, from /usr/include/c++/13/bits/streambuf_iterator.h:35, from /usr/include/c++/13/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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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 file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX static library 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/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 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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target input In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/alloc_traits.h:39, from /usr/include/c++/13/ext/alloc_traits.h:34, from /usr/include/c++/13/bits/hashtable_policy.h:39, from /usr/include/c++/13/bits/hashtable.h:35, from /usr/include/c++/13/bits/unordered_map.h:33, from /usr/include/c++/13/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/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++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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::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)...); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/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::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 = 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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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 member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/alloc_traits.h:39, from /usr/include/c++/13/ext/alloc_traits.h:34, from /usr/include/c++/13/bits/hashtable_policy.h:39, from /usr/include/c++/13/bits/hashtable.h:35, from /usr/include/c++/13/bits/unordered_map.h:33, from /usr/include/c++/13/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /usr/include/c++/13/bits/shared_ptr_atomic.h:33, from /usr/include/c++/13/memory:81, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/binary.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:14, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10: In member function 'std::__atomic_base<_IntTp>::__int_type std::__atomic_base<_IntTp>::fetch_add(__int_type, std::memory_order) [with _ITp = int]', inlined from 'void llvm::ThreadSafeRefCountedBase::Retain() const [with Derived = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:94:43, inlined from 'static void llvm::IntrusiveRefCntPtrInfo::retain(T*) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:125:43, inlined from 'void llvm::IntrusiveRefCntPtr::retain() [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:184:40, inlined from 'llvm::IntrusiveRefCntPtr::IntrusiveRefCntPtr(const llvm::IntrusiveRefCntPtr&) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:143:72, inlined from 'Sequence::Sequence(const Sequence&, size_t, size_t, bool)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:132:52, inlined from 'Sequence::Sequence(const Sequence&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:174:51, inlined from 'void boost::optional_detail::optional_base::construct(rval_reference_type) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:357:8, inlined from 'void boost::optional_detail::optional_base::assign(boost::optional_detail::optional_base&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:234:20, inlined from 'boost::optional& boost::optional::operator=(boost::optional&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:954:21, inlined from 'omnigraph::GapDescription& omnigraph::GapDescription::operator=(omnigraph::GapDescription&&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:24:7, inlined from 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1824:17: /usr/include/c++/13/bits/atomic_base.h:635:35: warning: '((llvm::IntrusiveRefCntPtr*)((char*)&__val + offsetof(omnigraph::value_type, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' may be used uninitialized [-Wmaybe-uninitialized] 635 | { return __atomic_fetch_add(&_M_i, __i, int(__m)); } | ^~~~~ In file included from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pointer_iterator.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1822:17: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__val + offsetof(omnigraph::value_type, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 1822 | __val = _GLIBCXX_MOVE(*__i); | ^~~~~ [ 81%] Linking CXX static library libmodules.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/modules.dir/link.txt --verbose=1 /usr/bin/ar qc libmodules.a CMakeFiles/modules.dir/chromosome_remover.cpp.o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/bin/ranlib libmodules.a In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target modules In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'std::__atomic_base<_IntTp>::__int_type std::__atomic_base<_IntTp>::fetch_add(__int_type, std::memory_order) [with _ITp = int]', inlined from 'void llvm::ThreadSafeRefCountedBase::Retain() const [with Derived = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:94:43, inlined from 'static void llvm::IntrusiveRefCntPtrInfo::retain(T*) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:125:43, inlined from 'void llvm::IntrusiveRefCntPtr::retain() [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:184:40, inlined from 'llvm::IntrusiveRefCntPtr::IntrusiveRefCntPtr(const llvm::IntrusiveRefCntPtr&) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:143:72, inlined from 'Sequence::Sequence(const Sequence&, size_t, size_t, bool)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:132:52, inlined from 'Sequence::Sequence(const Sequence&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:174:51, inlined from 'void boost::optional_detail::optional_base::construct(rval_reference_type) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:357:8, inlined from 'void boost::optional_detail::optional_base::assign(boost::optional_detail::optional_base&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:234:20, inlined from 'boost::optional& boost::optional::operator=(boost::optional&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:954:21, inlined from 'omnigraph::GapDescription& omnigraph::GapDescription::operator=(omnigraph::GapDescription&&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:24:7, inlined from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = omnigraph::GapDescription]' at /usr/include/c++/13/bits/move.h:199:11: /usr/include/c++/13/bits/atomic_base.h:635:35: warning: '((llvm::IntrusiveRefCntPtr*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' may be used uninitialized [-Wmaybe-uninitialized] 635 | { return __atomic_fetch_add(&_M_i, __i, int(__m)); } | ^~~~~ In file included from /usr/include/c++/13/bits/exception_ptr.h:41, from /usr/include/c++/13/exception:164, from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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: /usr/include/c++/13/bits/move.h: In function 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = omnigraph::GapDescription]': /usr/include/c++/13/bits/move.h:197:11: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In member function 'std::__atomic_base<_IntTp>::__int_type std::__atomic_base<_IntTp>::fetch_add(__int_type, std::memory_order) [with _ITp = int]', inlined from 'void llvm::ThreadSafeRefCountedBase::Retain() const [with Derived = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:94:43, inlined from 'static void llvm::IntrusiveRefCntPtrInfo::retain(T*) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:125:43, inlined from 'void llvm::IntrusiveRefCntPtr::retain() [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:184:40, inlined from 'llvm::IntrusiveRefCntPtr::IntrusiveRefCntPtr(const llvm::IntrusiveRefCntPtr&) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:143:72, inlined from 'Sequence::Sequence(const Sequence&, size_t, size_t, bool)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:132:52, inlined from 'Sequence::Sequence(const Sequence&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:174:51, inlined from 'void boost::optional_detail::optional_base::construct(rval_reference_type) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:357:8, inlined from 'void boost::optional_detail::optional_base::assign(boost::optional_detail::optional_base&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:234:20, inlined from 'boost::optional& boost::optional::operator=(boost::optional&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:954:21, inlined from 'omnigraph::GapDescription& omnigraph::GapDescription::operator=(omnigraph::GapDescription&&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:24:7, inlined from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = omnigraph::GapDescription]' at /usr/include/c++/13/bits/move.h:199:11, inlined from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator*, vector > >; _ForwardIterator2 = __gnu_cxx::__normal_iterator*, vector > >]' at /usr/include/c++/13/bits/stl_algobase.h:185:11, inlined from '_RandomAccessIterator std::__unguarded_partition(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1884:18, inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1899:40, inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1931:38: /usr/include/c++/13/bits/atomic_base.h:635:35: warning: '((llvm::IntrusiveRefCntPtr*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' may be used uninitialized [-Wmaybe-uninitialized] 635 | { return __atomic_fetch_add(&_M_i, __i, int(__m)); } | ^~~~~ /usr/include/c++/13/bits/move.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/move.h:197:11: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In member function 'std::__atomic_base<_IntTp>::__int_type std::__atomic_base<_IntTp>::fetch_add(__int_type, std::memory_order) [with _ITp = int]', inlined from 'void llvm::ThreadSafeRefCountedBase::Retain() const [with Derived = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:94:43, inlined from 'static void llvm::IntrusiveRefCntPtrInfo::retain(T*) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:125:43, inlined from 'void llvm::IntrusiveRefCntPtr::retain() [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:184:40, inlined from 'llvm::IntrusiveRefCntPtr::IntrusiveRefCntPtr(const llvm::IntrusiveRefCntPtr&) [with T = Sequence::ManagedNuclBuffer]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/llvm/ADT/IntrusiveRefCntPtr.h:143:72, inlined from 'Sequence::Sequence(const Sequence&, size_t, size_t, bool)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:132:52, inlined from 'Sequence::Sequence(const Sequence&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence.hpp:174:51, inlined from 'void boost::optional_detail::optional_base::construct(rval_reference_type) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:357:8, inlined from 'boost::optional_detail::optional_base::optional_base(boost::optional_detail::optional_base&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:173:18, inlined from 'boost::optional::optional(boost::optional&&) [with T = Sequence]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/boost/optional/optional.hpp:884:29, inlined from 'omnigraph::GapDescription::GapDescription(omnigraph::GapDescription&&)' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:24:7, inlined from 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_heap.h:264:25, inlined from 'void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_heap.h:425:19, inlined from 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1911:23, inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1926:27: /usr/include/c++/13/bits/atomic_base.h:635:35: warning: '((llvm::IntrusiveRefCntPtr*)((char*)&__value + offsetof(omnigraph::_ValueType, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' may be used uninitialized [-Wmaybe-uninitialized] 635 | { return __atomic_fetch_add(&_M_i, __i, int(__m)); } | ^~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:262:18: note: '((llvm::IntrusiveRefCntPtr*)((char*)&__value + offsetof(omnigraph::_ValueType, omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)))[1].llvm::IntrusiveRefCntPtr::Obj' was declared here 262 | _ValueType __value = _GLIBCXX_MOVE(*__result); | ^~~~~~~ [ 81%] Linking CXX static library libpath_extend.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/path_extend.dir/link.txt --verbose=1 /usr/bin/ar qc libpath_extend.a CMakeFiles/path_extend.dir/pe_config_struct.cpp.o CMakeFiles/path_extend.dir/loop_detector.cpp.o CMakeFiles/path_extend.dir/loop_traverser.cpp.o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o CMakeFiles/path_extend.dir/path_extenders.cpp.o CMakeFiles/path_extend.dir/pe_resolver.cpp.o CMakeFiles/path_extend.dir/overlap_remover.cpp.o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o /usr/bin/ranlib libpath_extend.a make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target path_extend 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' [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o [ 82%] 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/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/pipeline/CMakeFiles/pipeline.dir/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 /build/reproducible-path/spades-3.15.5+dfsg/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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.hpp:5, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ [ 82%] Linking CXX static library libspades-stages.a cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" /usr/bin/ranlib libspades-stages.a /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target spades-stages /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/alloc_traits.h:39, from /usr/include/c++/13/ext/alloc_traits.h:34, from /usr/include/c++/13/bits/hashtable_policy.h:39, from /usr/include/c++/13/bits/hashtable.h:35, from /usr/include/c++/13/bits/unordered_map.h:33, from /usr/include/c++/13/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 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 '/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/ionhammer /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/ionhammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: 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[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' [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.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/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 [ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.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_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/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 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT common/stages/CMakeFiles/stages.dir/construction.cpp.o -MF CMakeFiles/stages.dir/construction.cpp.o.d -o CMakeFiles/stages.dir/construction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/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 [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o [ 84%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o [ 86%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o [ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -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 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 CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp 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/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/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 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 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 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 85 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 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/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/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 >]' /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>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:172:102: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/HSeq.hpp:93:36: warning: unused parameter 'size' [-Wunused-parameter] 93 | static size_t GetDataSize(size_t size) { | ~~~~~~~^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp:357:110: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, 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/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_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/construction.cpp: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/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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:328:94: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:345:28: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:83:52: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/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]' /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]' /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 >&)>]' /usr/include/c++/13/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 >&)>&}]' /usr/include/c++/13/bits/alloc_traits.h:661:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/13/bits/shared_ptr_base.h:971:16: 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]' /usr/include/c++/13/bits/shared_ptr_base.h:1712:14: 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]' /usr/include/c++/13/bits/shared_ptr.h:464:59: 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]' /usr/include/c++/13/bits/shared_ptr.h:1009:14: 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< >::value), _Tp>::type = omnigraph::ComplexTipClipper]' /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 >&)>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:248:42: required from here /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]' /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]' /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]' /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]' /usr/include/c++/13/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 >&}]' /usr/include/c++/13/bits/alloc_traits.h:661:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/13/bits/shared_ptr_base.h:971:16: 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]' /usr/include/c++/13/bits/shared_ptr_base.h:1712:14: 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]' /usr/include/c++/13/bits/shared_ptr.h:464:59: 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]' /usr/include/c++/13/bits/shared_ptr.h:1009:14: 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< >::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /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 >&)>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:237:57: required from here /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, 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/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /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]' /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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /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]' /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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /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 /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 /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 /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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.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 "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-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a 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, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/alloc_traits.h:39, from /usr/include/c++/13/ext/alloc_traits.h:34, from /usr/include/c++/13/bits/hashtable_policy.h:39, from /usr/include/c++/13/bits/hashtable.h:35, from /usr/include/c++/13/bits/unordered_map.h:33, from /usr/include/c++/13/unordered_map:41, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/pack.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/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++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 344 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 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 -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake "--color=" make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake "--color=" make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake "--color=" make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake "--color=" make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake "--color=" make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend make[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/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake "--color=" make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake "--color=" make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake "--color=" make -f projects/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/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 -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/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake "--color=" make -f projects/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/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]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake "--color=" make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake "--color=" make[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]: 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[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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'/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build 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/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build 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/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build 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' 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' 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' make[4]: Entering 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 -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' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: 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/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' [ 87%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o [ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o [ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o [ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o [ 87%] 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/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 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 [ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o [ 88%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.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 [ 88%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o [ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o [ 88%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o [ 89%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o [ 89%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o [ 89%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o [ 89%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o [ 89%] 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/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 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 [ 90%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o [ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.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/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 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 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 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/config_struct_hammer.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 [ 91%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.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/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 [ 91%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp [ 93%] 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/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 [ 94%] 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/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 [ 94%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 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 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 [ 95%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o [ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o [ 96%] 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/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 [ 96%] 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/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 [ 96%] 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/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 [ 96%] 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/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 [ 96%] 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/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:12: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp: In instantiation of 'void parallel_radix_sort::value_manager::PairValueManager::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:54:26: required from 'std::pair SubKMerSplitter::split(Op&&) [with Op = KMerHamClusterer::cluster(const std::string&, const KMerData&, dsu::ConcurrentDSU&)::::iterator&, size_t)>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp:147:21: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:42: warning: unused parameter 'num_elems' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~~~~^~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/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; | ^~~~ /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&) 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/projects/bin_analysis/main.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] 248 | EdgeSet ProcessComponent(const VertexSet &reached, | ~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 275 | for (EdgeId e : annotated) { | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] 465 | for (EdgeId e : annotated) { | ^ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] 103 | const bool using_edge_qual = edge_qual.IsAttached(); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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 /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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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; | ^~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8: /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]' /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]' /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]' /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]' /usr/include/c++/13/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 >&}]' /usr/include/c++/13/bits/alloc_traits.h:661:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/13/bits/shared_ptr_base.h:971:16: 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]' /usr/include/c++/13/bits/shared_ptr_base.h:1712:14: 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]' /usr/include/c++/13/bits/shared_ptr.h:464:59: 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]' /usr/include/c++/13/bits/shared_ptr.h:1009:14: 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< >::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /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 >&)>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:157:65: required from here /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/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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 /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /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/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] [ 96%] Linking CXX executable ../../bin/spades-core cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:548, from /usr/include/c++/13/cstring:42, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, 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'; | ^~~~ [ 96%] Linking CXX executable ../../bin/spades-corrector-core cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [ 96%] Linking CXX executable ../../bin/spades-truseq-scfcorrection cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-corrector-core 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[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-truseq-scfcorrection make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target spades-core /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ [ 97%] Linking CXX executable ../../bin/spades-hammer [ 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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ 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 make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-hammer [ 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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target spades-kmer-estimating /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ [ 97%] Linking CXX executable ../../bin/spades-kmercount cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ [ 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 In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-kmercount [ 98%] Linking CXX executable ../../bin/form_truealignments cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-read-filter make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target form_truealignments /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ [ 98%] Linking CXX executable ../../bin/spades-gmapper cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [ 98%] Linking CXX executable ../../bin/spaligner cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-gmapper make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spaligner [100%] Linking CXX executable ../../bin/cds-subgraphs cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [100%] Linking CXX executable ../../bin/unitig-coverage cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-subgraphs make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target unitig-coverage /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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/cds-mapping-stats cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-mapping-stats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-mapping-stats.dir/stats.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-mapping-stats ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-mapping-stats /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/spades-gbuilder cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-gbuilder [100%] Linking CXX executable ../../bin/mag-improve cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so 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 "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-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target spades-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 -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake "--color=" make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake "--color=" make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make -f ext/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/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake "--color=" make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/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/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 /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/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=" 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 "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/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/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/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/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/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 "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". 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/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/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 "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/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/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 "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/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/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". Consolidate compiler generated dependencies of target mimalloc-obj 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 "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/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". Consolidate compiler generated dependencies of target gqf 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 "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 "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/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/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". Consolidate compiler generated dependencies of target version 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 "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/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". Consolidate compiler generated dependencies of target edlib 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". Consolidate compiler generated dependencies of target format 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' 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". make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build 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". make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build 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". make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". 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 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 "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". make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build 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". make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build Consolidate compiler generated dependencies of target gtest 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/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/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/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 "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". make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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". make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build 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/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/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/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". 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/edlib/CMakeFiles/edlib.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' 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/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/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". 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' 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/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/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/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/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/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/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". 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' 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". Consolidate compiler generated dependencies of target coverage_model 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/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". Consolidate compiler generated dependencies of target binary_io 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/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/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/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/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/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". make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". 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 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". make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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/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/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/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/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/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/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/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/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/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". Consolidate compiler generated dependencies of target paired_info 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". make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build 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". make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/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". 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' [ 4%] Built target edlib [ 4%] Built target version [ 9%] Built target format [ 9%] Built target gqf [ 11%] Built target mimalloc-obj make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend [ 11%] Built target gtest make[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 -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 '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' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake "--color=" [ 11%] Built target binary_io [ 11%] Built target coverage_model Consolidate compiler generated dependencies of target BamTools 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 [ 11%] Built target paired_info 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_gtest.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/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/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". 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". Consolidate compiler generated dependencies of target sequence 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". 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' 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 -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.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/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target utils 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 -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 ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build [ 14%] Built target sequence [ 16%] Built target teamcity_gtest [ 33%] Built target BamTools 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' 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]: 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' [ 35%] Built target utils Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/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". [ 57%] Built target llvm-support make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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=" 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 -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' Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". 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". [ 64%] Built target samtools 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". 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=" 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". Consolidate compiler generated dependencies of target assembly_graph 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". 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 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/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". 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' 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/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 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/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=" [ 73%] Built target input 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/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/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/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/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/compiler_depend.internal". Dependencies file "common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_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/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/sequence_mapper.cpp.o.d" is newer than depends file "/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". Dependencies file "common/modules/path_extend/CMakeFiles/path_extend.dir/pe_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_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' Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build [ 78%] Built target modules make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 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 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-I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -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 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/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 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/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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 [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/paired_info_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o [100%] 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/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 [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 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test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/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/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/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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test.cpp /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); | ^~~~~~ /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_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:84:57: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:46:38: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/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/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_TrivialTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 104 | gap_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 115 | ends_cfg.penalty_ratio = 0.1; | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 153 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 183 | if (g.int_id(*it) == eid_int){ | ~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] 191 | gap_cfg.penalty_ratio = 0.1; | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /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 /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_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/paired_info_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:176:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:14: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:77:37: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphWithIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&, EdgeIndex&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:75:28: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:119:17: required from 'void debruijn_graph::RandomGraph::PerformRandomOperation() [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:112:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, 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/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:125:55: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:59:23: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraphUsingExtensionIndex(const config::debruijn_config::construction&, fs::impl::TmpDir, io::ReadStreamList&, Graph&) [with Read = io::SingleRead; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:68:45: required from 'debruijn_graph::KMerFiles debruijn_graph::ConstructGraph(const config::debruijn_config::construction&, fs::impl::TmpDir, Streams&, Graph&) [with Streams = io::ReadStreamList; KMerFiles = kmers::KMerDiskStorage >; fs::impl::TmpDir = llvm::IntrusiveRefCntPtr; Graph = DeBruijnGraph]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp:138:19: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 488 | graph.ereserve(size_t(2.01*sequences.size())); | ~~~~~~~~~~~~~~^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/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_iterators.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In 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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds=] 565 | ++vptr; | ^~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /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]' /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]' /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]' /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]' /usr/include/c++/13/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 >&}]' /usr/include/c++/13/bits/alloc_traits.h:661:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/13/bits/shared_ptr_base.h:971:16: 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]' /usr/include/c++/13/bits/shared_ptr_base.h:1712:14: 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]' /usr/include/c++/13/bits/shared_ptr.h:464:59: 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]' /usr/include/c++/13/bits/shared_ptr.h:1009:14: 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< >::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' /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 >&)>]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:312:83: required from here /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, 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/test/debruijn/path_extend_test.cpp:8: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 30 | bool loaded = Base::Load(basename, graph); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] 43 | bool loaded = Base::BinRead(is, graph); | ^~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:18: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp: In instantiation of 'omnigraph::ParallelBulgeRemover::SmartEdgeSet omnigraph::ParallelBulgeRemover::RetainIndependentBulges(std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; SmartEdgeSet = omnigraph::SmartSetIterator >]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:720:42: required from 'size_t omnigraph::ParallelBulgeRemover::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:677:12: required from here /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 >]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:353:12: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1057:10: required from here /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]' /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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /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]' /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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /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/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /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]' /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]' /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]' /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]' /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1189:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 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, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:11: /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] 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 /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/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/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 /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 /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:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:7: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ 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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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::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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger.hpp:10, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/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++/13/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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/bits/new_allocator.h:151:55: note: object of size 504 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In 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++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 577 | *mutable_child(i) = c; | ~~~~~~~~~~~~~~~~~~^~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/quality.hpp:18, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/io/reads/single_read.hpp:11, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.hpp:9, from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/debruijn/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++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::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++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:578:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds=] 578 | c->fields_.parent = this; | ~~~~~~~~~~~~~~~~~~^~~~~~ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = char]', inlined from 'btree::btree::node_type* btree::btree::new_internal_node(node_type*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:1281:47, inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2150:33: /usr/include/c++/13/bits/new_allocator.h:151:55: note: object of size 384 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 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, | ^~~~~~~~~~~~~ [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 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/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/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/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/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build 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[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make -f common/utils/CMakeFiles/version.dir/build.make 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]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[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 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/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 '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]: 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]: 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/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/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/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' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build [ 9%] Built target edlib [ 9%] Built target gqf [ 9%] Built target format [ 9%] 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 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. [ 12%] Built target mimalloc-obj 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 make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend [ 12%] Built target gtest make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/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=" [ 12%] Built target coverage_model [ 12%] Built target binary_io make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd 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'/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' 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 '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]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target llvm-support 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' 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 [ 56%] Built target sequence [ 56%] Built target teamcity_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/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 58%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend [ 65%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/spades-3.15.5+dfsg/assembler/src /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/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=" 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/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 70%] Built target input [ 75%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend 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 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/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' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o [ 97%] 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/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion 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-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 cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp cd /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/include -I/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common -I/build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/reproducible-path/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/reproducible-path/spades-3.15.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++14 -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp In file included from /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:7: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/reproducible-path/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, 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 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-16/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libzstd.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-16/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[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 -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu 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. (0 ms total) 1: [ PASSED ] 58 tests. 1/2 Test #1: include_test ..................... Passed 0.00 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 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 / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.Empty (0 ms) 2: [ RUN ] GraphCore.OneVertex 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) 2: [----------] 6 tests from GraphCore (0 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic 2: [ OK ] Histogram.StrongWeakPtrBasic (0 ms) 2: [----------] 1 test from Histogram (0 ms total) 2: 2: [----------] 13 tests from PairedInfo 2: [ RUN ] PairedInfo.Construct 2: [ OK ] PairedInfo.Construct (0 ms) 2: [ RUN ] PairedInfo.Access 2: [ OK ] PairedInfo.Access (0 ms) 2: [ RUN ] PairedInfo.HalfAccess 2: [ OK ] PairedInfo.HalfAccess (0 ms) 2: [ RUN ] PairedInfo.Remove 2: [ OK ] PairedInfo.Remove (0 ms) 2: [ RUN ] PairedInfo.UnexistingEdges 2: [ OK ] PairedInfo.UnexistingEdges (0 ms) 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours 2: [ OK ] PairedInfo.Neighbours (0 ms) 2: [ RUN ] PairedInfo.DoubledInfo 2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours 2: [ OK ] PairedInfo.HalfNeighbours (0 ms) 2: [ RUN ] PairedInfo.MoreNeighbours 2: [ OK ] PairedInfo.MoreNeighbours (0 ms) 2: [ RUN ] PairedInfo.Merge 2: [ OK ] PairedInfo.Merge (0 ms) 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.000 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] PairedInfo.RandomSymmetry (36 ms) 2: [----------] 13 tests from PairedInfo (36 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: 0:00:00.037 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.037 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp 2: 0:00:00.038 1M / 9M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started 2: 0:00:00.039 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip 2: [ OK ] Simplification.SimpleTipClipperTest (3 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest 2: 0:00:00.040 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.040 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.040 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: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.040 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.SimpleBulgeRemovalTest (1 ms) 2: [ RUN ] Simplification.TipobulgeTest 2: 0:00:00.040 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.040 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.040 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.041 1M / 14M INFO General (graph_simplification.hpp : 645) Creating br instance 2: [ OK ] Simplification.TipobulgeTest (0 ms) 2: [ RUN ] Simplification.SimpleECTest 2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.041 1M / 14M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.041 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: 0:00:00.041 1M / 14M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.066 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleECTest (41 ms) 2: [ RUN ] Simplification.SimpleIterECTest 2: 0:00:00.082 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.082 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.082 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp 2: 0:00:00.082 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started 2: 0:00:00.098 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.SimpleIterECTest (37 ms) 2: [ RUN ] Simplification.IterECTest 2: 0:00:00.119 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.119 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.119 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: 0:00:00.119 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: 0:00:00.136 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: [ OK ] Simplification.IterECTest (33 ms) 2: [ RUN ] Simplification.IterUniquePath 2: 0:00:00.152 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.152 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.152 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: 0:00:00.152 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: 0:00:00.169 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path 2: 0:00:00.169 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology 2: 0:00:00.177 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology 2: [ OK ] Simplification.IterUniquePath (40 ms) 2: [ RUN ] Simplification.MFUniquePath 2: 0:00:00.192 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.192 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.192 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: 0:00:00.192 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started 2: 0:00:00.203 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path 2: 0:00:00.203 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy 2: [ OK ] Simplification.MFUniquePath (41 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge 2: 0:00:00.233 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.233 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.233 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: 0:00:00.233 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started 2: 0:00:00.233 1M / 61M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge 2: 0:00:00.233 1M / 61M INFO General (simplification_test.cpp : 276) Done 2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (1 ms) 2: [ RUN ] Simplification.ComplexBulge 2: 0:00:00.234 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.234 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.234 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.234 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.234 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.250 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.250 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) 2: 0:00:00.277 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.335 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: 0:00:00.335 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.363 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.364 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: [ OK ] Simplification.ComplexBulge (158 ms) 2: [ RUN ] Simplification.BigComplexBulge 2: 0:00:00.392 1M / 64M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.392 1M / 64M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.392 1M / 64M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.392 1M / 64M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp 2: 0:00:00.392 1M / 64M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.502 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge 2: 0:00:00.503 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) 2: 0:00:00.524 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.563 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). 2: 0:00:00.563 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.590 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started 2: 0:00:00.590 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 (227 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover 2: 0:00:00.619 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.619 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.619 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.619 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp 2: 0:00:00.619 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.620 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.620 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) 2: 0:00:00.625 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.658 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). 2: 0:00:00.658 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.669 2M / 154M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started 2: 0:00:00.669 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph 2: 0:00:00.669 2M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover (91 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 2: 0:00:00.710 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.710 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.710 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.710 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp 2: 0:00:00.710 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.730 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.730 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) 2: 0:00:00.757 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.815 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: 0:00:00.816 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.844 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started 2: 0:00:00.844 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge 2: 0:00:00.844 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover1 (161 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 2: 0:00:00.871 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.871 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.871 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.871 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp 2: 0:00:00.871 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started 2: 0:00:00.871 3M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:00.871 3M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) 2: 0:00:00.872 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.873 3M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). 2: 0:00:00.874 3M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.874 3M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:00.874 3M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph 2: 0:00:00.874 3M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover2 (12 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 2: 0:00:00.883 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.883 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.883 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.883 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp 2: 0:00:00.883 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started 2: 0:00:00.883 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.883 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) 2: 0:00:00.883 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.883 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). 2: 0:00:00.883 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.884 1M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:00.884 1M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge 2: 0:00:00.884 1M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover3 (2 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 2: 0:00:00.885 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.885 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.885 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.885 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp 2: 0:00:00.885 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started 2: 0:00:00.885 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:00.885 4M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) 2: 0:00:00.886 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.891 4M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). 2: 0:00:00.891 4M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.893 4M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:00.893 4M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph 2: 0:00:00.893 4M / 154M INFO General (simplification_test.cpp : 308) Relative coverage component removal: 2: [ OK ] Simplification.RelativeCoverageRemover4 (21 ms) 2: [ RUN ] Simplification.CompressorTest 2: 0:00:00.905 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.905 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.905 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.905 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp 2: 0:00:00.905 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started 2: 0:00:00.906 2M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: 0:00:00.906 2M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) 2: 0:00:00.906 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.906 2M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). 2: 0:00:00.906 2M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.906 2M / 154M INFO General (graphio.cpp : 185) No positions were saved 2: 0:00:00.906 2M / 154M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph 2: [ OK ] Simplification.CompressorTest (1 ms) 2: [----------] 17 tests from Simplification (870 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread 2: 0:00:00.907 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.907 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.907 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.907 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.907 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.907 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.907 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.914 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 2 reads 2: 0:00:00.914 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.915 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. 2: 0:00:00.915 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.915 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.915 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.915 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.915 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.917 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. 2: 0:00:00.917 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.919 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. 2: 0:00:00.919 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.919 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). 2: 0:00:00.919 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.920 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.920 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.920 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.920 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:00.920 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread (14 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 2: 0:00:00.920 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.920 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.920 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.920 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.920 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.921 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.921 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.923 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:00.923 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.924 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. 2: 0:00:00.924 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.924 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.924 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.924 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.924 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.927 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. 2: 0:00:00.927 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.928 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. 2: 0:00:00.928 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.928 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). 2: 0:00:00.928 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.929 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.929 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.929 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted 2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.929 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:00.929 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SimpleThread2 (9 ms) 2: [ RUN ] GraphConstruction.SplitThread 2: 0:00:00.930 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.930 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.930 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.930 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.930 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.930 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.930 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.932 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:00.932 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.933 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.933 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.933 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.933 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.933 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.933 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.936 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. 2: 0:00:00.936 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.937 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.937 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.938 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:00.938 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.938 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.938 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.938 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:00.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.938 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create 2: 0:00:00.939 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread (9 ms) 2: [ RUN ] GraphConstruction.SplitThread2 2: 0:00:00.939 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.939 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.939 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.939 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.939 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.939 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.939 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.941 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:00.941 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.943 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.943 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.943 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.943 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.943 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.943 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.945 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. 2: 0:00:00.945 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.946 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. 2: 0:00:00.946 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.947 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). 2: 0:00:00.947 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.947 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.948 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.948 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.948 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.948 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted 2: 0:00:00.948 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.948 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create 2: 0:00:00.948 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.SplitThread2 (9 ms) 2: [ RUN ] GraphConstruction.Buldge 2: 0:00:00.948 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.948 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.948 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.948 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.948 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.948 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.948 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.951 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:00.951 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.952 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.952 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.952 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.952 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.952 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.952 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.954 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. 2: 0:00:00.954 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.956 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. 2: 0:00:00.956 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.956 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). 2: 0:00:00.956 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.957 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.957 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.957 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.957 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.957 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted 2: 0:00:00.957 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.957 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create 2: 0:00:00.957 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.Buldge (10 ms) 2: [ RUN ] GraphConstruction.CondenseSimple 2: 0:00:00.957 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.957 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.957 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.957 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.958 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.958 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.958 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.960 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:00.961 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.962 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.962 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.962 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.962 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.962 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.962 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.964 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:00.964 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.966 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.966 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.966 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:00.966 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.967 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.967 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.967 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.967 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.967 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:00.967 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.967 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:00.967 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: [ OK ] GraphConstruction.CondenseSimple (11 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex 2: 0:00:00.968 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.968 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.968 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.968 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.968 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.968 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.968 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.969 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.971 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:00.971 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.972 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.972 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.972 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.972 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.972 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.972 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.975 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:00.975 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.976 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.976 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.976 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:00.976 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.977 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.977 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.977 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.977 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.977 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:00.977 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.977 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:00.977 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:00.977 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:00.977 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) 2: 0:00:00.977 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.978 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:00.978 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerStoringIndex (9 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex 2: 0:00:00.978 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.978 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.978 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.978 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 2: 0:00:00.978 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.978 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.978 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.978 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.980 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 8 reads 2: 0:00:00.980 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.982 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.982 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.982 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.982 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.982 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.982 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.984 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. 2: 0:00:00.984 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.985 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. 2: 0:00:00.985 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.986 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). 2: 0:00:00.986 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.986 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.987 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.987 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.987 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.987 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted 2: 0:00:00.987 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.987 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create 2: 0:00:00.987 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:00.987 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:00.987 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) 2: 0:00:00.987 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.987 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). 2: 0:00:00.987 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: [ OK ] GraphConstruction.TestKmerFreeIndex (9 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo 2: 0:00:00.987 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:00.987 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:00.987 1M / 154M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 2: 0:00:00.987 1M / 154M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 2: 0:00:00.987 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.987 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.987 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.987 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.990 1M / 154M INFO General (kmer_splitters.hpp : 131) Used 4 reads 2: 0:00:00.990 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.991 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. 2: 0:00:00.991 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 2: 0:00:00.991 1M / 154M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. 2: 0:00:00.991 1M / 154M INFO General (file_limit.hpp : 42) Open file limit set to 1024 2: 0:00:00.991 1M / 154M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb 2: 0:00:00.991 1M / 154M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 2: 0:00:00.993 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. 2: 0:00:00.993 1M / 154M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 2: 0:00:00.995 1M / 154M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. 2: 0:00:00.995 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.995 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: 0:00:00.995 1M / 154M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 2: 0:00:00.995 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 2: 0:00:00.995 1M / 154M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 2: 0:00:00.995 1M / 154M INFO General (graph_construction.hpp : 57) Condensing graph 2: 0:00:00.996 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 2: 0:00:00.996 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted 2: 0:00:00.996 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 2: 0:00:00.996 1M / 154M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 489) Collecting link records 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 491) Ordering link records 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 493) Sorting done 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create 2: 0:00:00.996 1M / 154M INFO General (debruijn_graph_constructor: 506) Connecting the graph 2: 0:00:00.996 1M / 154M INFO General (graph_construction.hpp : 79) Building index with from graph 2: 0:00:00.996 1M / 154M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) 2: 0:00:00.996 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.996 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: 0:00:00.996 1M / 154M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. 2: 0:00:00.996 1M / 154M INFO General (graph_construction.hpp : 93) Filling coverage index 2: 0:00:00.996 1M / 154M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 2: 0:00:00.996 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: 0:00:00.996 1M / 154M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 2: 0:00:00.996 1M / 154M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM 2: 0:00:00.996 1M / 154M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process 2: 0:00:00.996 1M / 154M INFO General (graph_pack.cpp : 79) Normalizing done 2: 0:00:01.000 10M / 154M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed 2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (16 ms) 2: [----------] 9 tests from GraphConstruction (97 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order 2: 0:00:01.003 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.003 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.039 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.039 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] Io.Order (35 ms) 2: [ RUN ] Io.PairedInfo 2: [ OK ] Io.PairedInfo (4 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (0 ms) 2: [----------] 3 tests from Io (39 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathConstructor (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemove (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.043 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.043 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.044 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: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.044 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.044 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector 2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) 2: [----------] 8 tests from PathExtend (2 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff 2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.045 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: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.045 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.045 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.046 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: 0:00:01.046 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.046 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.046 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp 2: 0:00:01.046 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started 2: 0:00:01.046 1M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation 2: 0:00:01.046 1M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat 2: 0:00:01.046 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.046 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.046 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.046 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.051 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.051 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeat (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven 2: 0:00:01.051 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.051 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.051 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.051 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.055 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.056 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatUneven (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected 2: 0:00:01.056 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.056 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.056 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.056 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.060 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.060 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.060 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect 2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.060 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.060 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.065 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.065 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd 2: 0:00:01.065 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.065 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.065 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.065 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.069 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.069 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.069 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEnd (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain 2: 0:00:01.070 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.070 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.070 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.070 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.074 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.074 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.074 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (4 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart 2: 0:00:01.074 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.074 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.074 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.074 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.079 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.079 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.079 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStart (5 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain 2: 0:00:01.079 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.079 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.079 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.079 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.083 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.083 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.083 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (5 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication 2: 0:00:01.083 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.083 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.084 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.084 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.088 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplication (4 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual 2: 0:00:01.088 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.088 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.088 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.088 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.093 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff 2: 0:00:01.093 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.093 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.093 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.093 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.097 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiff (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap 2: 0:00:01.097 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.097 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.097 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.097 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.102 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateDiffGap (4 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 2: 0:00:01.102 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.102 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.102 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.102 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.107 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (5 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 2: 0:00:01.107 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.107 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.107 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.107 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.111 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (5 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen 2: 0:00:01.111 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.111 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.111 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.111 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.116 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.116 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.116 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (4 ms) 2: [ RUN ] OverlapRemoval.Tricky0 2: 0:00:01.116 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.116 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.116 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.116 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.120 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.120 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.120 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky0 (5 ms) 2: [ RUN ] OverlapRemoval.Tricky1 2: 0:00:01.121 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.121 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.121 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.121 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.125 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.125 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.125 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky1 (4 ms) 2: [ RUN ] OverlapRemoval.Tricky2 2: 0:00:01.125 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.125 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.125 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.125 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.130 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.130 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.130 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.Tricky2 (5 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen 2: 0:00:01.130 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.130 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.130 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.130 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.134 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.134 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.134 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.BasicMinEdgeLen (5 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle 2: 0:00:01.135 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.135 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.135 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.135 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.139 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.139 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps 2: 0:00:01.139 4M / 154M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps 2: [ OK ] OverlapRemoval.OverlapWithMiddle (4 ms) 2: [----------] 23 tests from OverlapRemoval (94 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest 2: 0:00:01.139 1M / 154M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero 2: 0:00:01.139 1M / 154M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 2: 0:00:01.139 1M / 154M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest 2: 0:00:01.139 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.139 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.139 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.139 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.144 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: 0:00:01.151 5M / 154M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm 2: [ OK ] GraphAligner.TrivialTest (425 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest 2: 0:00:01.564 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.564 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.564 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.564 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.569 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraOneEdgeTest (5 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest 2: 0:00:01.569 1M / 154M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 2: 0:00:01.569 1M / 154M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: 0:00:01.569 1M / 154M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp 2: 0:00:01.569 1M / 154M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started 2: 0:00:01.573 4M / 154M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation 2: [ OK ] GraphAligner.DijkstraGrowEndsTest (5 ms) 2: [----------] 5 tests from GraphAligner (435 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 98 tests from 10 test suites ran. (1574 ms total) 2: [ PASSED ] 98 tests. 2/2 Test #2: debruijn_test .................... Passed 1.58 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.59 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 -j42 install DESTDIR=/build/reproducible-path/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/spades-3.15.5+dfsg/assembler/src -B/build/reproducible-path/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall 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.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.txt -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset/operons_1K.gff -- 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/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/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/B_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_truspades/B_R1.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/pl1.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/TE.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AT.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KS.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/KR.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/AMP.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/biosynthetic_spades_hmms/CStart.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/coronaspades_hmms/Phan-CoV.hmm.gz -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/manual.html -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/README.md -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/truspades_manual.html -- Installing: /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/hmm_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/metaplasmid_mode.info -- 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-- 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/moleculo_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/rnaviral_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/config.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/isolate_mode.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/configs/debruijn/toy.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: 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/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/postprocessing_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/copy_files.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/check_test_script.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//scripts/preprocess_interlaced_reads.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/before_start_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/spades_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/preprocess_reads_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/error_correction_stage.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//stages/spades_iteration_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/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/pipeline.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/moleculo_postprocessing.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/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/__init__.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/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/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/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/__init__.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//common/alignment.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//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/executor_local.py -- Installing: /build/reproducible-path/spades-3.15.5+dfsg/debian/spades/usr/share/spades/spades_pipeline//executors/executors.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-dbgsym' in '../spades-dbgsym_3.15.5+dfsg-7_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_3.15.5+dfsg-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../spades_3.15.5+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../spades_3.15.5+dfsg-7_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/4087328/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4087328/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/4087328 and its subdirectories I: Current time: Fri Jun 13 23:49:14 +14 2025 I: pbuilder-time-stamp: 1749808154