I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 11 19:36:58 -12 2023 I: pbuilder-time-stamp: 1676187418 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_3.13.1+dfsg-2.dsc] I: copying [./spades_3.13.1+dfsg.orig.tar.xz] I: copying [./spades_3.13.1+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.M9ftsnOO/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 21 21:49:38 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./spades_3.13.1+dfsg-2.dsc dpkg-source: info: extracting spades in spades-3.13.1+dfsg dpkg-source: info: unpacking spades_3.13.1+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.13.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 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 0110_build_single_thread.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0115_enable_compiler_messages.patch dpkg-source: info: applying 0111_use_full_config_dirs.patch dpkg-source: info: applying 0116_stable_link_order.patch dpkg-source: info: applying 0117_build_with_debug.patch dpkg-source: info: applying 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying spelling dpkg-source: info: applying gcc7.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1777496/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3191333a33a94739977cb5084186d29b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1777496' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.QpjsReePDq/pbuilderrc_2hAm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.QpjsReePDq/b1 --logfile b1/build.log spades_3.13.1+dfsg-2.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Feb 9 03:46 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/1777496/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 (= 12), dh-python, cmake, python3-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python3-yaml, python3-joblib, asciidoctor (>= 1.5.3), 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 ... 19655 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev 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 libboost-dev; however: Package libboost-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 libhat-trie-dev; however: Package libhat-trie-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 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 (>= 1.5.3); 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} 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} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbam-dev{a} libbamtools-dev{a} libbamtools2.5.1{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libbwa-dev{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libhat-trie-dev{a} libhat-trie0{a} libhts-dev{a} libhts3{a} libicu67{a} libidn11{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp24{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libnlopt-cxx-dev{a} libnlopt-cxx0{a} libnlopt-dev{a} libnlopt0{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libyaml-0-2{a} lynx{a} lynx-common{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} procps{a} python3{a} python3-dev{a} python3-distutils{a} python3-joblib{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-yaml{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc fonts-lato javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules mime-support psmisc publicsuffix python3-numpy python3-psutil python3-pytest python3-simplejson zip 0 packages upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 67.1 MB of archives. After unpacking 348 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 rubygems-integration all 1.18 [6704 B] Get: 29 http://deb.debian.org/debian bullseye/main amd64 rake all 13.0.3-1 [84.7 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libruby2.7 amd64 2.7.4-1 [4200 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 ruby2.7 amd64 2.7.4-1 [747 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 ruby amd64 1:2.7+2 [11.7 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 bwa amd64 0.7.17-6+b1 [212 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libbam-dev amd64 0.1.19+dfsg-2 [118 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-9 [158 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libbamtools-dev amd64 2.5.1+dfsg-9 [208 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libbwa-dev amd64 0.7.17-6+b1 [143 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libexpat1-dev amd64 2.2.10-2 [140 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libhat-trie-dev amd64 0.1.2-2 [19.9 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libidn11 amd64 1.33-3 [116 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libnlopt0 amd64 2.7.0-4+b2 [172 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libnlopt-dev amd64 2.7.0-4+b2 [29.8 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libnlopt-cxx0 amd64 2.7.0-4+b2 [200 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libnlopt-cxx-dev amd64 2.7.0-4+b2 [14.5 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-dev amd64 3.9.2-1 [4028 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libssw0 amd64 1.1-13 [19.7 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libssw-dev amd64 1.1-13 [22.4 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 lynx-common all 2.9.0dev.6-3~deb11u1 [1192 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 lynx amd64 2.9.0dev.6-3~deb11u1 [652 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 python3.9-dev amd64 3.9.2-1 [515 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4 [213 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Fetched 67.1 MB in 1s (62.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../2-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20943 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../002-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_1.1.1k-1+deb11u1_amd64.deb ... Unpacking openssl (1.1.1k-1+deb11u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../008-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../011-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../012-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../013-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../014-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../015-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../016-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../017-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../018-libmd0_1.0.3-3_amd64.deb ... Unpacking libmd0:amd64 (1.0.3-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../019-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../020-libedit2_3.1-20191231-2+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-2+b1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../021-libyaml-0-2_0.2.2-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.2-1) ... Selecting previously unselected package libruby2.7:amd64. Preparing to unpack .../022-libruby2.7_2.7.4-1_amd64.deb ... Unpacking libruby2.7:amd64 (2.7.4-1) ... Selecting previously unselected package ruby2.7. Preparing to unpack .../023-ruby2.7_2.7.4-1_amd64.deb ... Unpacking ruby2.7 (2.7.4-1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../024-ruby-rubygems_3.2.5-2_all.deb ... Unpacking ruby-rubygems (3.2.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../025-ruby_1%3a2.7+2_amd64.deb ... Unpacking ruby (1:2.7+2) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../026-ruby-asciidoctor_2.0.12-2_all.deb ... Unpacking ruby-asciidoctor (2.0.12-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../027-asciidoctor_2.0.12-2_all.deb ... Unpacking asciidoctor (2.0.12-2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../028-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../029-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../030-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../031-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../032-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../033-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bwa. Preparing to unpack .../034-bwa_0.7.17-6+b1_amd64.deb ... Unpacking bwa (0.7.17-6+b1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../035-cmake-data_3.18.4-2+deb11u1_all.deb ... Unpacking cmake-data (3.18.4-2+deb11u1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../036-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../037-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../038-libarchive13_3.4.3-2+b1_amd64.deb ... Unpacking libarchive13:amd64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../039-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../040-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../041-libsasl2-2_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../042-libldap-2.4-2_2.4.57+dfsg-3_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../043-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../044-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../045-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../046-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../047-libcurl4_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libjsoncpp24:amd64. Preparing to unpack .../048-libjsoncpp24_1.9.4-4_amd64.deb ... Unpacking libjsoncpp24:amd64 (1.9.4-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../049-librhash0_1.4.1-2_amd64.deb ... Unpacking librhash0:amd64 (1.4.1-2) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../050-libuv1_1.40.0-2_amd64.deb ... Unpacking libuv1:amd64 (1.40.0-2) ... Selecting previously unselected package cmake. 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Setting up libbam-dev (0.1.19+dfsg-2) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Setting up lynx (2.9.0dev.6-3~deb11u1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.11-4) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... 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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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/spades-3.13.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_3.13.1+dfsg-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --sourcedirectory=assembler/src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/spades-3.13.1+dfsg' dh_auto_clean rm -rf build_spades rm -rf install_spades rm -rf spades_test find . -name "*.pyc" -delete rm -rf /build/spades-3.13.1+dfsg/debian/man_src/*.html /build/spades-3.13.1+dfsg/debian/man_src/*.? rm -rf /build/spades-3.13.1+dfsg/debian/man make[1]: Leaving directory '/build/spades-3.13.1+dfsg' dh_autoreconf_clean -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/spades-3.13.1+dfsg' dh_clean -X.orig make[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules build dh build --with python3 --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/spades-3.13.1+dfsg' echo "Simply use spades_compile.sh in auto_build" Simply use spades_compile.sh in auto_build make[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/spades-3.13.1+dfsg' cd assembler && PREFIX=/build/spades-3.13.1+dfsg/install_spades ./spades_compile.sh 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. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- 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 CMake Warning (dev) at cmake/options.cmake:56 (set): implicitly converting 'INTEGER' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/options.cmake:57 (set): implicitly converting 'INTEGER' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- 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 "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message): The package name passed to `find_package_handle_standard_args` (readline) does not match the name of the calling package (Readline). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/Modules/FindReadline.cmake:32 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) cmake/deps.cmake:19 (find_package) CMakeLists.txt:52 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Looking for include file features.h -- Looking for include file features.h - found -- Looking for include file sys/cdefs.h -- Looking for include file sys/cdefs.h - found -- Looking for atomic_fetchadd_long -- Looking for atomic_fetchadd_long - not found -- Looking for OSAtomicAdd64 -- Looking for OSAtomicAdd64 - not found -- Looking for OSSpinLockLock -- Looking for OSSpinLockLock - not found -- Looking for _malloc_thread_cleanup -- Looking for _malloc_thread_cleanup - not found -- Looking for _pthread_mutex_init_calloc_cb, -- Looking for _pthread_mutex_init_calloc_cb, - not found -- Looking for sbrk -- Looking for sbrk - found -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Performing Test JEMALLOC_TLS -- Performing Test JEMALLOC_TLS - Success -- Looking for memalign -- Looking for memalign - found -- Looking for valloc -- Looking for valloc - found -- Check size of int -- Check size of int - done -- Check size of long -- Check size of long - done -- Check size of intmax_t -- Check size of intmax_t - done -- Looking for open -- Looking for open - found -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Looking for include file signal.h -- Looking for include file signal.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file cxxabi.h -- Looking for include file cxxabi.h - not found -- Looking for include file dlfcn.h -- Looking for include file dlfcn.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - not found -- Looking for include file link.h -- Looking for include file link.h - found -- Looking for backtrace -- Looking for backtrace - found -- Configuring done -- Generating done -- Build files have been written to: /build/spades-3.13.1+dfsg/assembler/build_spades make[2]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' /usr/bin/cmake -S/build/spades-3.13.1+dfsg/assembler/src -B/build/spades-3.13.1+dfsg/assembler/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-3.13.1+dfsg/assembler/build_spades/CMakeFiles /build/spades-3.13.1+dfsg/assembler/build_spades//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". Scanning dependencies of target jemalloc make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/arena.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/arena.c [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/base.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/base.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/base.c [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/chunk.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_mmap.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_mmap.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/chunk_mmap.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ctl.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ctl.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/ctl.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/hash.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/hash.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/hash.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/jemalloc.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/jemalloc.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/jemalloc.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mutex.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mutex.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/mutex.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/quarantine.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/quarantine.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/quarantine.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/stats.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/stats.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/stats.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tsd.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tsd.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/tsd.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/atomic.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/atomic.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/atomic.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/bitmap.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/bitmap.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/bitmap.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_dss.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_dss.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/chunk_dss.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ckh.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ckh.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/ckh.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/extent.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/extent.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/extent.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/huge.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/huge.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/huge.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mb.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mb.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/mb.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/prof.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/prof.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/prof.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/rtree.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/rtree.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/rtree.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tcache.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tcache.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/tcache.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/util.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc -I/build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/util.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c: In function 'malloc_vsnprintf': /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:339:2: warning: case label value exceeds maximum value for type [-Wswitch-outside-range] 339 | case '?' | 0x80: \ | ^~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:551:5: note: in expansion of macro 'GET_ARG_NUMERIC' 551 | GET_ARG_NUMERIC(val, 'p'); | ^~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:345:2: warning: case label value exceeds maximum value for type [-Wswitch-outside-range] 345 | case 'l' | 0x80: \ | ^~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:551:5: note: in expansion of macro 'GET_ARG_NUMERIC' 551 | GET_ARG_NUMERIC(val, 'p'); | ^~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:351:2: warning: case label value exceeds maximum value for type [-Wswitch-outside-range] 351 | case 'q' | 0x80: \ | ^~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:551:5: note: in expansion of macro 'GET_ARG_NUMERIC' 551 | GET_ARG_NUMERIC(val, 'p'); | ^~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:363:2: warning: case label value exceeds maximum value for type [-Wswitch-outside-range] 363 | case 'z' | 0x80: \ | ^~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/jemalloc/util.c:551:5: note: in expansion of macro 'GET_ARG_NUMERIC' 551 | GET_ARG_NUMERIC(val, 'p'); | ^~~~~~~~~~~~~~~ [ 9%] Linking C static library libjemalloc.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cmake -P CMakeFiles/jemalloc.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/jemalloc && /usr/bin/cmake -E cmake_link_script CMakeFiles/jemalloc.dir/link.txt --verbose=1 /usr/bin/ar qc libjemalloc.a CMakeFiles/jemalloc.dir/arena.c.o CMakeFiles/jemalloc.dir/base.c.o CMakeFiles/jemalloc.dir/chunk.c.o CMakeFiles/jemalloc.dir/chunk_mmap.c.o CMakeFiles/jemalloc.dir/ctl.c.o CMakeFiles/jemalloc.dir/hash.c.o CMakeFiles/jemalloc.dir/jemalloc.c.o CMakeFiles/jemalloc.dir/mutex.c.o CMakeFiles/jemalloc.dir/quarantine.c.o CMakeFiles/jemalloc.dir/stats.c.o CMakeFiles/jemalloc.dir/tsd.c.o CMakeFiles/jemalloc.dir/atomic.c.o CMakeFiles/jemalloc.dir/bitmap.c.o CMakeFiles/jemalloc.dir/chunk_dss.c.o CMakeFiles/jemalloc.dir/ckh.c.o CMakeFiles/jemalloc.dir/extent.c.o CMakeFiles/jemalloc.dir/huge.c.o CMakeFiles/jemalloc.dir/mb.c.o CMakeFiles/jemalloc.dir/prof.c.o CMakeFiles/jemalloc.dir/rtree.c.o CMakeFiles/jemalloc.dir/tcache.c.o CMakeFiles/jemalloc.dir/util.c.o /usr/bin/ranlib libjemalloc.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 9%] Built target jemalloc make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Scanning dependencies of target ConsensusCore make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 9%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp [ 10%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp [ 10%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp [ 10%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/PairwiseAlignment.cpp [ 11%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp [ 11%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp [ 11%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore/Version.cpp [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src 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-I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp [ 21%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp [ 21%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/BamFile_p.cpp [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp [ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp [ 25%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /build/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:2: note: in expansion of macro '_bgzf_read' 578 | _bgzf_read(fp->fp, buf, 28); | ^~~~~~~~~~ [ 26%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /build/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:2: note: in expansion of macro 'netwrite' 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /build/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:2: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ [ 26%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /build/spades-3.13.1+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); | ^~~~~~~~~~~ [ 26%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined 240 | unpackInt16(const uint8_t* buffer); | ^~~~~~~~~~~ [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /build/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: At top level: /build/spades-3.13.1+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/spades-3.13.1+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /build/spades-3.13.1+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); | ^~~~~~~~~~~ [ 28%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c [ 28%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /build/spades-3.13.1+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); | ^~~~~~~~~~~ [ 28%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp [ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp [ 29%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp [ 30%] Linking CXX static library libBamTools.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd 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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 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Scanning dependencies of target samtools make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 30%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. 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-Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam.c [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_import.c [ 33%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/sam.c [ 33%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:178:35: 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; | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:335:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:342:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:355:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:358:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:362:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:366:4: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:376:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_index.c:380:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_pileup.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_lpileup.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_md.c [ 34%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/razf.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:221:3: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:234:4: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:201:3: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:804:4: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:805:4: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:808:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:810:4: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:258:4: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:96:12: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:99:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:106:2: 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/spades-3.13.1+dfsg/assembler/ext/src/samtools/razf.c:107:2: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/faidx.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/faidx.c [ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bedidx.c [ 35%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_sort.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/sam_header.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_reheader.c [ 36%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/kprobaln.c [ 38%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools -I/build/spades-3.13.1+dfsg/assembler/ext/src/samtools -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/samtools/bam_cat.c [ 38%] Linking CXX static library libsamtools.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o /usr/bin/ranlib libsamtools.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 38%] Built target samtools make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/cppformat /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". Scanning dependencies of target format make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 38%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat -I/build/spades-3.13.1+dfsg/assembler/ext/src/cppformat -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/format.cc.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/cppformat/format.cc [ 39%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat -I/build/spades-3.13.1+dfsg/assembler/ext/src/cppformat -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/posix.cc.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/cppformat/posix.cc [ 39%] Linking CXX static library libformat.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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 /usr/bin/ranlib libformat.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 39%] Built target format make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/cityhash /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/depend.internal". Scanning dependencies of target cityhash make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 39%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash -I/build/spades-3.13.1+dfsg/assembler/ext/src/cityhash -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/cityhash.dir/city.cc.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/cityhash/city.cc [ 40%] Linking CXX static library libcityhash.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash && /usr/bin/cmake -P CMakeFiles/cityhash.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/cityhash && /usr/bin/cmake -E cmake_link_script CMakeFiles/cityhash.dir/link.txt --verbose=1 /usr/bin/ar qc libcityhash.a CMakeFiles/cityhash.dir/city.cc.o /usr/bin/ranlib libcityhash.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 40%] Built target cityhash make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp /build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". Scanning dependencies of target getopt_pp make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 40%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp -I/build/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp [ 41%] Linking CXX static library libgetopt_pp.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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 /usr/bin/ranlib libgetopt_pp.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 41%] Built target getopt_pp make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/llvm /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". Scanning dependencies of target llvm-support make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Atomic.cpp [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Hashing.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/LineIterator.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Mutex.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Mutex.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Mutex.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Path.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Regex.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ 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-I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/SourceMgr.cpp [ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/StringMap.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/StringRef.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/Twine.cpp [ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/YAMLParser.cpp [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp [ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/raw_ostream.cpp [ 48%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/regcomp.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG 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/build/spades-3.13.1+dfsg/assembler/ext/src/llvm/regexec.c [ 50%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/regfree.c [ 51%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm -I/build/spades-3.13.1+dfsg/assembler/ext/src/llvm -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/llvm/regstrlcpy.c [ 51%] Linking CXX static library libllvm-support.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/Atomic.cpp.o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o CMakeFiles/llvm-support.dir/Hashing.cpp.o CMakeFiles/llvm-support.dir/LineIterator.cpp.o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o CMakeFiles/llvm-support.dir/Mutex.cpp.o CMakeFiles/llvm-support.dir/Path.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/StringMap.cpp.o CMakeFiles/llvm-support.dir/StringRef.cpp.o CMakeFiles/llvm-support.dir/Twine.cpp.o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o CMakeFiles/llvm-support.dir/regcomp.c.o CMakeFiles/llvm-support.dir/regerror.c.o CMakeFiles/llvm-support.dir/regexec.c.o CMakeFiles/llvm-support.dir/regfree.c.o CMakeFiles/llvm-support.dir/regstrlcpy.c.o /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 51%] Built target llvm-support make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/gqf /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Scanning dependencies of target gqf make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 52%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf -I/build/spades-3.13.1+dfsg/assembler/ext/src/gqf -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gqf.dir/gqf.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:614:16: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 614 | printf("%02llx ", j); | ~~~~~^ ~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lx /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump': /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:645:13: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 645 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 646 | qf->metadata->nblocks, | ~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:645:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 645 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu 646 | qf->metadata->nblocks, 647 | qf->metadata->ndistinct_elts, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:645:23: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 645 | printf("%llu %llu %llu\n", | ~~~^ | | | long long unsigned int | %lu ...... 648 | qf->metadata->nelts); | ~~~~~~~~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_init': /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1451:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 1451 | fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); | ~~~^ ~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1451:27: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 1451 | fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1451:32: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 1451 | fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1477:31: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 1477 | fprintf(stderr, "nslots: %llu\n", qf->metadata->range); | ~~~^ ~~~~~~~~~~~~~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1479:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 1479 | fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1479:59: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] 1479 | fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); | ~~~~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %016lx /build/spades-3.13.1+dfsg/assembler/ext/include/gqf/gqf.h: In function 'qf_deserialize': /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1610:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1610 | fread(qf->metadata, sizeof(qfmetadata), 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/ext/src/gqf/gqf.c:1619:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1619 | fread(qf->blocks, qf->metadata->size, 1, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Linking C static library libgqf.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 52%] Built target gqf make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/edlib /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib /build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Scanning dependencies of target edlib make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib -I/build/spades-3.13.1+dfsg/assembler/ext/src/edlib -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/edlib.dir/edlib.cpp.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/edlib/edlib.cpp [ 53%] Linking CXX static library libedlib.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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 /usr/bin/ranlib libedlib.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target edlib make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/ext/src/gfa1 /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Scanning dependencies of target gfa1 make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 -I/build/spades-3.13.1+dfsg/assembler/ext/src/gfa1 -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/spades-3.13.1+dfsg/assembler/ext/src/gfa1/gfa.c [ 53%] Linking C static library libgfa1.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 /usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o /usr/bin/ranlib libgfa1.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target gfa1 make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Scanning dependencies of target coverage_model make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' 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/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp /build/spades-3.13.1+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /build/spades-3.13.1+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/spades-3.13.1+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_ ? | ^~~~~~~ [ 54%] Linking CXX static library libcoverage_model.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 /usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o /usr/bin/ranlib libcoverage_model.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 54%] Built target coverage_model make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/io /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/io /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Scanning dependencies of target input make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 54%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/reads/parser.cpp [ 55%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/sam/read.cpp [ 55%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io -I/build/spades-3.13.1+dfsg/assembler/src/common/io -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/sam/sam_reader.cpp [ 55%] Linking CXX static library libinput.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 55%] Built target input make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/pipeline /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Scanning dependencies of target pipeline make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 57%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:817:19: required from 'void debruijn_graph::graphio::PrintAll(const string&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:34:44: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:527:41: required from 'bool debruijn_graph::graphio::DataScanner::LoadPositions(const string&, omnigraph::EdgesPositionHandler&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:900:26: required from 'void debruijn_graph::graphio::ScanGraphPack(const string&, debruijn_graph::graphio::DataScanner&, graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:1057:18: required from 'void debruijn_graph::graphio::ScanAll(const string&, graph_pack&, bool) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:527:41: required from 'bool debruijn_graph::graphio::DataScanner::LoadPositions(const string&, omnigraph::EdgesPositionHandler&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:900:26: required from 'void debruijn_graph::graphio::ScanGraphPack(const string&, debruijn_graph::graphio::DataScanner&, graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:1057:18: required from 'void debruijn_graph::graphio::ScanAll(const string&, graph_pack&, bool) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:527:41: required from 'bool debruijn_graph::graphio::DataScanner::LoadPositions(const string&, omnigraph::EdgesPositionHandler&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:900:26: required from 'void debruijn_graph::graphio::ScanGraphPack(const string&, debruijn_graph::graphio::DataScanner&, graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:1057:18: required from 'void debruijn_graph::graphio::ScanAll(const string&, graph_pack&, bool) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:24:50: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:817:19: required from 'void debruijn_graph::graphio::PrintAll(const string&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:34:44: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 57%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/config_struct.cpp [ 57%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/genomic_info_filler.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 58%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/common/pipeline -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/library.cpp [ 58%] Linking CXX static library libpipeline.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/pipeline && /usr/bin/cmake -P CMakeFiles/pipeline.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/stage.cpp.o CMakeFiles/pipeline.dir/config_struct.cpp.o CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o CMakeFiles/pipeline.dir/library.cpp.o /usr/bin/ranlib libpipeline.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 58%] Built target pipeline make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/sequence /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/sequence /build/spades-3.13.1+dfsg/assembler/build_spades/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= Dependee 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Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph/CMakeFiles/assembly_graph.dir/depend.internal". 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-fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp [ 60%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp [ 61%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, from /usr/include/boost/algorithm/string.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 61%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/io/reads/header_naming.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/io/utils/edge_namer.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 61%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp: In member function 'bool path_extend::ScaffoldingUniqueEdgeAnalyzer::ConservativeByPaths(path_extend::EdgeId, const path_extend::GraphCoverageMap&, const path_extend::pe_config::LongReads&, int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:130:13: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 130 | if (maxx < lr_config.unique_edge_priority * double(alt)) { | ^~~~ [ 63%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp: In instantiation of 'size_t utils::IndexWrapper::raw_seq_idx(typename utils::IndexWrapper::KMerIndexT::KMerRawReference) const [with K = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; typename utils::IndexWrapper::KMerIndexT::KMerRawReference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:238:44: required from 'void utils::KeyStoringMap::SortUniqueKMers() const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:79:30: required from 'void utils::KeyStoringIndexBuilder::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:111:40: required from 'void utils::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:104:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&, fs::TmpDir, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; fs::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:44:39: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 44 | return index_ptr_->raw_seq_idx(s); | ~~~~~~~~~~~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:86:45: note: initializing argument 1 of 'size_t utils::KMerIndex::raw_seq_idx(utils::KMerIndex::KMerRawReference) const [with traits = utils::kmer_index_traits >; size_t = long unsigned int; utils::KMerIndex::KMerRawReference = adt::array_reference >]' 86 | size_t raw_seq_idx(const KMerRawReference data) const { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp: In instantiation of 'size_t utils::KMerIndex::raw_seq_idx(utils::KMerIndex::KMerRawReference) const [with traits = utils::kmer_index_traits >; size_t = long unsigned int; utils::KMerIndex::KMerRawReference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:44:39: required from 'size_t utils::IndexWrapper::raw_seq_idx(typename utils::IndexWrapper::KMerIndexT::KMerRawReference) const [with K = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; typename utils::IndexWrapper::KMerIndexT::KMerRawReference = adt::array_reference >]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:238:44: required from 'void utils::KeyStoringMap::SortUniqueKMers() const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:79:30: required from 'void utils::KeyStoringIndexBuilder::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:111:40: required from 'void utils::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:104:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&, fs::TmpDir, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; fs::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:87:35: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 87 | size_t bucket = raw_seq_bucket(data); | ~~~~~~~~~~~~~~^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:132:48: note: initializing argument 1 of 'size_t utils::KMerIndex::raw_seq_bucket(utils::KMerIndex::KMerRawReference) const [with traits = utils::kmer_index_traits >; size_t = long unsigned int; utils::KMerIndex::KMerRawReference = adt::array_reference >]' 132 | size_t raw_seq_bucket(const KMerRawReference data) const { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:89:58: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 89 | return bucket_starts_[bucket] + index_[bucket].lookup(data); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/ext/include/boomphf/BooPHF.h:808:28: note: initializing argument 1 of 'uint64_t boomphf::mphf::lookup(elem_t) [with elem_t = adt::array_reference >; Hasher_t = utils::KMerIndex > >::hash_function128; uint64_t = long unsigned int]' 808 | uint64_t lookup(elem_t elem) { | ~~~~~~~^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp: In instantiation of 'size_t utils::KMerIndex::raw_seq_bucket(utils::KMerIndex::KMerRawReference) const [with traits = utils::kmer_index_traits >; size_t = long unsigned int; utils::KMerIndex::KMerRawReference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:87:21: required from 'size_t utils::KMerIndex::raw_seq_idx(utils::KMerIndex::KMerRawReference) const [with traits = utils::kmer_index_traits >; size_t = long unsigned int; utils::KMerIndex::KMerRawReference = adt::array_reference >]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:44:39: required from 'size_t utils::IndexWrapper::raw_seq_idx(typename utils::IndexWrapper::KMerIndexT::KMerRawReference) const [with K = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; typename utils::IndexWrapper::KMerIndexT::KMerRawReference = adt::array_reference >]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:238:44: required from 'void utils::KeyStoringMap::SortUniqueKMers() const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:79:30: required from 'void utils::KeyStoringIndexBuilder::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map_builder.hpp:111:40: required from 'void utils::BuildIndex(utils::KeyStoringMap&, Counter&, size_t, size_t, bool) [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; Counter = utils::KMerDiskCounter >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:104:19: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&, fs::TmpDir, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; fs::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:133:27: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 133 | return hash_function()(data) % num_buckets_; | ~~~~~~~~~~~~~~~^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:43:48: note: initializing argument 1 of 'uint64_t utils::kmer_index_traits::hash_function::operator()(utils::kmer_index_traits::KMerRawReference, uint64_t) const [with Seq = RuntimeSeq<128>; uint64_t = long unsigned int; utils::kmer_index_traits::KMerRawReference = adt::array_reference >]' 43 | uint64_t operator()(const KMerRawReference k, uint64_t seed = 0) const { | ~~~~~~~~~~~~~~~~~~~~~~~^ /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp: In instantiation of 'bool utils::kmer_index_traits::raw_equal_to::operator()(const Seq&, utils::kmer_index_traits::KMerRawReference) [with Seq = RuntimeSeq<128>; utils::kmer_index_traits::KMerRawReference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:312:54: required from 'bool utils::KeyStoringMap::valid(const KeyWithHash&) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; utils::KeyStoringMap::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:123:23: required from 'bool debruijn_graph::DeBruijnEdgeMultiIndex::contains(const KeyWithHash&) const [with IdType = restricted::pure_pointer >; Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; debruijn_graph::DeBruijnEdgeMultiIndex::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:134:12: required from 'void debruijn_graph::DeBruijnEdgeMultiIndex::PutInIndex(const KeyWithHash&, IdType, size_t) [with IdType = restricted::pure_pointer >; Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; debruijn_graph::DeBruijnEdgeMultiIndex::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:51:30: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateKMers(const Sequence&, debruijn_graph::EdgeInfoUpdater::EdgeId) [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::EdgeInfoUpdater::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:82:9: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateKmers(debruijn_graph::EdgeInfoUpdater::EdgeId) [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::EdgeInfoUpdater::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:100:17: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateAll() [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:109:26: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&, fs::TmpDir, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; fs::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:26:60: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 26 | return (adt::array_equal_to()(lhs.data(), lhs.data_size(), rhs)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:678:65: note: initializing argument 3 of 'bool adt::array_equal_to::operator()(const ElTy*, size_t, adt::array_equal_to::reference) const [with ElTy = long unsigned int; size_t = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]' 678 | bool operator()(const ElTy *lhs, size_t sz, const reference rhs) const { | ~~~~~~~~~~~~~~~~^~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(const ElTy*, size_t, adt::array_equal_to::reference) const [with ElTy = long unsigned int; size_t = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:26:60: required from 'bool utils::kmer_index_traits::raw_equal_to::operator()(const Seq&, utils::kmer_index_traits::KMerRawReference) [with Seq = RuntimeSeq<128>; utils::kmer_index_traits::KMerRawReference = adt::array_reference >]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:312:54: required from 'bool utils::KeyStoringMap::valid(const KeyWithHash&) const [with K = RuntimeSeq<128>; V = debruijn_graph::EdgeInfoStorage > >; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; utils::KeyStoringMap::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:123:23: required from 'bool debruijn_graph::DeBruijnEdgeMultiIndex::contains(const KeyWithHash&) const [with IdType = restricted::pure_pointer >; Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; debruijn_graph::DeBruijnEdgeMultiIndex::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:134:12: required from 'void debruijn_graph::DeBruijnEdgeMultiIndex::PutInIndex(const KeyWithHash&, IdType, size_t) [with IdType = restricted::pure_pointer >; Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; StoringType = utils::SimpleStoring; debruijn_graph::DeBruijnEdgeMultiIndex::KeyWithHash = utils::SimpleKeyWithHash, utils::KMerIndex > > >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:51:30: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateKMers(const Sequence&, debruijn_graph::EdgeInfoUpdater::EdgeId) [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::EdgeInfoUpdater::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:82:9: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateKmers(debruijn_graph::EdgeInfoUpdater::EdgeId) [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph; debruijn_graph::EdgeInfoUpdater::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:100:17: required from 'void debruijn_graph::EdgeInfoUpdater::UpdateAll() [with Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:109:26: required from 'void debruijn_graph::GraphPositionFillingIndexBuilder::BuildIndexFromGraph(Index&, const Graph&, fs::TmpDir, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; Index = debruijn_graph::DeBruijnEdgeMultiIndex > >; fs::TmpDir = llvm::IntrusiveRefCntPtr; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:35:52: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:679:41: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 679 | return const_reference(lhs, sz) == rhs; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:350:48: note: initializing argument 1 of 'bool adt::array_const_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 350 | bool operator==(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:74:26: required from 'typename utils::DeBruijnKMerSplitter::RawKMers debruijn_graph::DeBruijnGraphKMerSplitter::Split(size_t, unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; KmerFilter = utils::StoringTypeFilter; typename utils::DeBruijnKMerSplitter::RawKMers = std::vector >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:74:26: required from 'typename utils::DeBruijnKMerSplitter::RawKMers debruijn_graph::DeBruijnGraphKMerSplitter::Split(size_t, unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; KmerFilter = utils::StoringTypeFilter; typename utils::DeBruijnKMerSplitter::RawKMers = std::vector >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:133:34: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:74:26: required from 'typename utils::DeBruijnKMerSplitter::RawKMers debruijn_graph::DeBruijnGraphKMerSplitter::Split(size_t, unsigned int) [with Graph = debruijn_graph::DeBruijnGraph; KmerFilter = utils::StoringTypeFilter; typename utils::DeBruijnKMerSplitter::RawKMers = std::vector >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:54:1: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 63%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp [ 63%] Linking CXX static library libassembly_graph.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/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/__/modules/alignment/edge_index_refiller.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o /usr/bin/ranlib libassembly_graph.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 63%] Built target assembly_graph make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend/CMakeFiles/path_extend.dir/depend.internal". Scanning dependencies of target path_extend make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 64%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp [ 64%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 64%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp: In constructor 'debruijn_graph::OverlapInfo::OverlapInfo(const Range&, const Range&, size_t)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp: In member function 'size_t path_extend::OverlapRemover::AnalyzeOverlaps(const path_extend::BidirectionalPath&, const path_extend::BidirectionalPath&, bool, bool) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:53:39: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 53 | auto other_range = range_pair.second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 65%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp: In constructor 'debruijn_graph::OverlapInfo::OverlapInfo(const Range&, const Range&, size_t)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 65%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+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/spades-3.13.1+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_) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp:6, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 66%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 66%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 66%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 67%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual std::map >, double> path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:102:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 102 | if (iter->second < min_read_count_){ | ^~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp:2, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 67%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp: In constructor 'debruijn_graph::OverlapInfo::OverlapInfo(const Range&, const Range&, size_t)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:2: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ [ 67%] Linking CXX static library libpath_extend.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/path_extend && /usr/bin/cmake -P CMakeFiles/path_extend.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/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/spades-3.13.1+dfsg/assembler/build_spades' [ 67%] Built target path_extend make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/modules /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules/CMakeFiles/modules.dir/depend.internal". Scanning dependencies of target modules make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 69%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp: In member function 'void debruijn_graph::GenomeConsistenceChecker::ClassifyPosition(size_t, size_t, const path_extend::BidirectionalPath&, debruijn_graph::PathScore&) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:281:58: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 281 | } else if (IsCloseToEnd(prev_range, prev_chr_info) && IsCloseToStart(cur_range, chr_info)) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:191:36: note: initializing argument 1 of 'bool debruijn_graph::GenomeConsistenceChecker::IsCloseToEnd(omnigraph::MappingRange, const debruijn_graph::ChromosomeInfo&) const' 191 | bool IsCloseToEnd(MappingRange range, const ChromosomeInfo &chr_info) const { | ~~~~~~~~~~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:281:97: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 281 | } else if (IsCloseToEnd(prev_range, prev_chr_info) && IsCloseToStart(cur_range, chr_info)) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:196:38: note: initializing argument 1 of 'bool debruijn_graph::GenomeConsistenceChecker::IsCloseToStart(omnigraph::MappingRange, const debruijn_graph::ChromosomeInfo&) const' 196 | bool IsCloseToStart(MappingRange range, const ChromosomeInfo &) const { | ~~~~~~~~~~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp: In member function 'std::vector debruijn_graph::GenomeConsistenceChecker::MappedRegions(const MappingPathT&) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:454:46: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 454 | auto current_range = mapping_path[i].second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:461:51: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 461 | auto prev_range = mapping_path[i - 1].second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp: In member function 'void debruijn_graph::GenomeConsistenceChecker::FillPos(path_extend::EdgeId, const omnigraph::EdgesPositionHandler&)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:488:60: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 488 | for (auto mp : tmp_edge_pos.GetEdgePositions(e, chr)) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 497 | gp_.edge_pos.AddEdgePosition(e, chr, mapping_info.first); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:119:70: note: initializing argument 3 of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' 119 | void AddEdgePosition(EdgeId edge, string contig_id, MappingRange new_pos) { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp: In member function 'std::pair debruijn_graph::GenomeConsistenceChecker::Merge(const std::vector&) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:503:38: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 503 | MappingRange mr = mappings.front(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:442:63: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:37:23: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const string&, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:400:57: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:497:60: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:442:63: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/stl_utils.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:183:25: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:141:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 141 | AddEdgePosition(edge, it->contigId, it->mr); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:119:70: note: initializing argument 3 of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' 119 | void AddEdgePosition(EdgeId edge, string contig_id, MappingRange new_pos) { | ~~~~~~~~~~~~~^~~~~~~ [ 69%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.cpp [ 69%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/common/modules -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 70%] Linking CXX static library libmodules.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/modules && /usr/bin/cmake -P CMakeFiles/modules.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/genome_consistance_checker.cpp.o CMakeFiles/modules.dir/alignment/gap_info.cpp.o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o /usr/bin/ranlib libmodules.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 70%] Built target modules make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/paired_info /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info/CMakeFiles/paired_info.dir/depend.internal". Scanning dependencies of target paired_info make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 70%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/distance_estimation.cpp [ 71%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp [ 71%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/common/paired_info -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp [ 71%] Linking CXX static library libpaired_info.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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 /usr/bin/ranlib libpaired_info.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 71%] Built target paired_info make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/stages /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages/CMakeFiles/stages.dir/depend.internal". Scanning dependencies of target stages make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 71%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/construction.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:209:57: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 209 | TRACE("Added to queue " << start_edges.back() << " " << mask); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:125:26: note: in definition of macro 'LOG_MSG' 125 | __logger__str__ << msg; /* don't use brackets here! */ \ | ^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:209:13: note: in expansion of macro 'TRACE' 209 | TRACE("Added to queue " << start_edges.back() << " " << mask); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:213:57: note: initializing argument 2 of 'stream& utils::operator<<(stream&, utils::AbstractDeEdge) [with stream = std::basic_ostream; KWH = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 213 | stream &operator<<(stream &s, const AbstractDeEdge de_edge) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdges(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, std::vector, utils::KMerIndex > > > > >&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:219:61: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 219 | AddStartDeEdgesForVertex(kh, extensions, start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:202:47: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const' 202 | void AddStartDeEdgesForVertex(KeyWithHash kh, utils::InOutMask mask, | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:223:49: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 223 | start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:202:47: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const' 202 | void AddStartDeEdgesForVertex(KeyWithHash kh, utils::InOutMask mask, | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'bool debruijn_graph::UnbranchingPathExtractor::StepRightIfPossible(debruijn_graph::UnbranchingPathExtractor::DeEdge&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 231 | origin_.GetOutgoing(edge.end, mask.GetUniqueOutgoing())); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:194:32: note: initializing argument 1 of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 194 | AbstractDeEdge(KeyWithHash s, KeyWithHash e) | ~~~~~~~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:241:26: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 241 | DeEdge initial = edge; | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'std::vector debruijn_graph::UnbranchingPathExtractor::ConstructLoopFromVertex(const KeyWithHash&, SequenceBuilder&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:257:61: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 257 | DeEdge break_point(kh, origin_.GetUniqueOutgoing(kh)); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:194:32: note: initializing argument 1 of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 194 | AbstractDeEdge(KeyWithHash s, KeyWithHash e) | ~~~~~~~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:258:68: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 258 | Sequence s = ConstructSequenceWithEdge(break_point, builder); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:237:47: note: initializing argument 1 of 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const' 237 | Sequence ConstructSequenceWithEdge(DeEdge edge, SequenceBuilder &builder) const { | ~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::CalculateSequences(debruijn_graph::UnbranchingPathExtractor::kmer_iterator&, std::vector&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:276:44: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 276 | AddStartDeEdges(kh, start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:213:38: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdges(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, std::vector, utils::KMerIndex > > > > >&) const' 213 | void AddStartDeEdges(KeyWithHash kh, std::vector& start_edges) const { | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:278:30: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 278 | for (auto edge : start_edges) { | ^~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:279:69: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 279 | Sequence s = ConstructSequenceWithEdge(edge, builder); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:237:47: note: initializing argument 1 of 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const' 237 | Sequence ConstructSequenceWithEdge(DeEdge edge, SequenceBuilder &builder) const { | ~~~~~~~^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:284:34: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 284 | TRACE("From " << edge << " calculated sequence\n" << s); | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:125:26: note: in definition of macro 'LOG_MSG' 125 | __logger__str__ << msg; /* don't use brackets here! */ \ | ^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:284:17: note: in expansion of macro 'TRACE' 284 | TRACE("From " << edge << " calculated sequence\n" << s); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:213:57: note: initializing argument 2 of 'stream& utils::operator<<(stream&, utils::AbstractDeEdge) [with stream = std::basic_ostream; KWH = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 213 | stream &operator<<(stream &s, const AbstractDeEdge de_edge) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'const std::vector debruijn_graph::UnbranchingPathExtractor::CollectLoops(unsigned int)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:319:35: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 319 | if (!IsJunction(kh)) | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:194:33: note: initializing argument 1 of 'bool debruijn_graph::UnbranchingPathExtractor::IsJunction(debruijn_graph::UnbranchingPathExtractor::KeyWithHash) const' 194 | bool IsJunction(KeyWithHash kwh) const { | ~~~~~~~~~~~~^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:328:35: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 328 | if (IsJunction(kwh)) | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:194:33: note: initializing argument 1 of 'bool debruijn_graph::UnbranchingPathExtractor::IsJunction(debruijn_graph::UnbranchingPathExtractor::KeyWithHash) const' 194 | bool IsJunction(KeyWithHash kwh) const { | ~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp: In member function 'size_t debruijn_graph::AlternativeEarlyTipClipper::RemoveForward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:125:54: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 125 | size_t len = FindForward(khc, tips[c]); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:76:36: note: initializing argument 1 of 'size_t debruijn_graph::AlternativeEarlyTipClipper::FindForward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash, std::vector, utils::KMerIndex > > > >&)' 76 | size_t FindForward(KeyWithHash kh, vector &tip) { | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp: In member function 'size_t debruijn_graph::AlternativeEarlyTipClipper::RemoveBackward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:140:55: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 140 | size_t len = FindBackward(khc, tips[c]); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:89:37: note: initializing argument 1 of 'size_t debruijn_graph::AlternativeEarlyTipClipper::FindBackward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash, std::vector, utils::KMerIndex > > > >&)' 89 | size_t FindBackward(KeyWithHash kh, vector &tip) { | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp: In member function 'size_t debruijn_graph::AlternativeEarlyTipClipper::RoughClipTips()': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:158:54: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 158 | result[i] += RemoveForward(kh); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:118:38: note: initializing argument 1 of 'size_t debruijn_graph::AlternativeEarlyTipClipper::RemoveForward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash)' 118 | size_t RemoveForward(KeyWithHash kh) { | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:161:55: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 161 | result[i] += RemoveBackward(kh); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/early_simplification.hpp:133:39: note: initializing argument 1 of 'size_t debruijn_graph::AlternativeEarlyTipClipper::RemoveBackward(debruijn_graph::AlternativeEarlyTipClipper::KeyWithHash)' 133 | size_t RemoveBackward(KeyWithHash kh) { | ~~~~~~~~~~~~^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp: In instantiation of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:195:52: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 195 | : start(std::move(s)), end(std::move(e)) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:21, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:195:52: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 195 | : start(std::move(s)), end(std::move(e)) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:261:19: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:261:19: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:265:28: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:198:73: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/graph_construction.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/construction.cpp:13: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 72%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:33, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/memory:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp: In instantiation of 'Range omnigraph::DominatedSetFinder::NeighbourDistanceRange(omnigraph::DominatedSetFinder::VertexId, bool) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::DominatedSetFinder::VertexId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:99:23: required from 'bool omnigraph::DominatedSetFinder::FillDominated() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:94:33: required from 'omnigraph::GraphComponent omnigraph::ComplexTipFinder::operator()(omnigraph::ComplexTipFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::ComplexTipFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+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 string&, omnigraph::ComplexTipClipper::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; std::string = std::__cxx11::basic_string; omnigraph::ComplexTipClipper::HandlerF = std::function >, std::less > >, std::allocator > > >&)>]' /usr/include/c++/10/ext/new_allocator.h:150:4: required from 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function >, std::less > >, std::allocator > > >&)>&}; _Tp = omnigraph::ComplexTipClipper]' /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::ComplexTipClipper; _Args = {debruijn_graph::DeBruijnGraph&, double&, long unsigned int&, long unsigned int, long unsigned int, const char (&)[1], std::function >, std::less > >, std::allocator > > >&)>&}; _Tp = omnigraph::ComplexTipClipper; std::allocator_traits >::allocator_type = std::allocator >]' /usr/include/c++/10/bits/shared_ptr_base.h:551:39: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/c++/10/bits/shared_ptr_base.h:1371:71: 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::less > >, std::allocator > > >&)>&}; _Tp = omnigraph::ComplexTipClipper; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' /usr/include/c++/10/bits/shared_ptr.h:408:59: 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::less > >, std::allocator > > >&)>&}; _Tp = omnigraph::ComplexTipClipper]' /usr/include/c++/10/bits/shared_ptr.h:859:14: required from 'std::shared_ptr<_Tp> std::allocate_shared(const _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::less > >, std::allocator > > >&)>&}]' /usr/include/c++/10/bits/shared_ptr.h:875:39: required from 'std::shared_ptr<_Tp> 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], std::function >, std::less > >, std::allocator > > >&)>&}]' /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:501:65: required from 'omnigraph::AlgoPtr debruijn::simplification::ComplexTipClipperInstance(Graph&, debruijn_graph::config::debruijn_config::simplification::complex_tip_clipper, const debruijn::simplification::SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function >, std::less > >, std::allocator > > >&)>]' /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:255:113: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:52:19: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 52 | Range range = dominated_.find(g_.EdgeStart(e))->second; | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/dominated_set_finder.hpp:63:16: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 63 | return answer; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'Range omnigraph::complex_br::LocalizedComponent::distance_range(omnigraph::complex_br::LocalizedComponent::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponent::VertexId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:956:37: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::CheckPathLengths() const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1024:14: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProceedFurther() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1068:42: required from 'bool omnigraph::complex_br::CandidateFinder::Check(omnigraph::complex_br::CandidateFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::CandidateFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:154:39: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 154 | return vertex_depth_.find(v)->second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'size_t omnigraph::complex_br::LocalizedComponent::avg_distance(omnigraph::complex_br::LocalizedComponent::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; omnigraph::complex_br::LocalizedComponent::VertexId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:966:53: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::CheckPositiveHeightDiff() const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1028:14: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProceedFurther() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1068:42: required from 'bool omnigraph::complex_br::CandidateFinder::Check(omnigraph::complex_br::CandidateFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::CandidateFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:159:23: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 159 | return Average(vertex_depth_.find(v)->second); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:57:26: note: initializing argument 1 of 'size_t omnigraph::complex_br::LocalizedComponent::Average(Range) const [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 57 | size_t Average(Range r) const { | ~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::LocalizedComponentFinder::AddVertexWithBackwardPaths(omnigraph::complex_br::LocalizedComponentFinder::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponentFinder::VertexId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:950:16: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProcessInterferingVertex(omnigraph::complex_br::LocalizedComponentFinder::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponentFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:981:18: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::CloseComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1012:22: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProceedFurther() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1068:42: required from 'bool omnigraph::complex_br::CandidateFinder::Check(omnigraph::complex_br::CandidateFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::CandidateFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:926:32: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 926 | comp_.AddVertex(next_v, dominated_.find(next_v)->second); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:84:38: note: initializing argument 2 of 'void omnigraph::complex_br::LocalizedComponent::AddVertex(omnigraph::complex_br::LocalizedComponent::VertexId, Range) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponent::VertexId = restricted::pure_pointer >]' 84 | void AddVertex(VertexId v, Range dist_range) { | ~~~~~~^~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::AddVertex(omnigraph::complex_br::LocalizedComponent::VertexId, Range) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponent::VertexId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:926:32: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::AddVertexWithBackwardPaths(omnigraph::complex_br::LocalizedComponentFinder::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponentFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:950:16: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProcessInterferingVertex(omnigraph::complex_br::LocalizedComponentFinder::VertexId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponentFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:981:18: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::CloseComponent() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1012:22: required from 'bool omnigraph::complex_br::LocalizedComponentFinder::ProceedFurther() [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1068:42: required from 'bool omnigraph::complex_br::CandidateFinder::Check(omnigraph::complex_br::CandidateFinder::VertexId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::CandidateFinder::VertexId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:1064:10: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:89:52: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 89 | height_2_vertices_.insert(make_pair(Average(dist_range), v)); | ~~~~~~~^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:57:26: note: initializing argument 1 of 'size_t omnigraph::complex_br::LocalizedComponent::Average(Range) const [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 57 | size_t Average(Range r) const { | ~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:138, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/basic_graph_stats.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:90:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 90 | DEBUG("Range " << dist_range << " Average height " << Average(dist_range)); | ~~~~~~~^~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:125:26: note: in definition of macro 'LOG_MSG' 125 | __logger__str__ << msg; /* don't use brackets here! */ \ | ^~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:90:9: note: in expansion of macro 'DEBUG' 90 | DEBUG("Range " << dist_range << " Average height " << Average(dist_range)); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:57:26: note: initializing argument 1 of 'size_t omnigraph::complex_br::LocalizedComponent::Average(Range) const [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 57 | size_t Average(Range r) const { | ~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::LocalizedComponent::HandleSplit(omnigraph::complex_br::LocalizedComponent::EdgeId, omnigraph::complex_br::LocalizedComponent::EdgeId, omnigraph::complex_br::LocalizedComponent::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::complex_br::LocalizedComponent::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:242:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:259:43: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 259 | std::make_pair(Average(new_vertex_depth), new_vertex)); | ~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_printer.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization_utils.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/visualization.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_tip_clipper.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:57:26: note: initializing argument 1 of 'size_t omnigraph::complex_br::LocalizedComponent::Average(Range) const [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' 57 | size_t Average(Range r) const { | ~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/parallel_simplification_algorithms.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/simplification/parallel_simplification_algorithms.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/simplification.cpp:11: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 72%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/common/stages -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp: In member function 'void debruijn_graph::SSBinCoverageFiller::ProcessRange(size_t, const omnigraph::MappingPath > >&)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:45: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 73 | auto range = read.mapping_at(i).mapped_range; | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:74:81: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 74 | tmp_storages_[thread_index].IncreaseKmerCount(read.edge_at(i), range); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:28, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage.hpp:241:44: note: initializing argument 2 of 'void debruijn_graph::SSCoverageSplitter::IncreaseKmerCount(debruijn_graph::EdgeId, Range)' 241 | void IncreaseKmerCount(EdgeId e, Range mapped_range) { | ~~~~~~^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::MappingPath::mapping_at(size_t) const [with ElementId = restricted::pure_pointer >; size_t = long unsigned int]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:43: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:236:35: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 236 | return range_mappings_[idx]; | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 72%] Linking CXX static library libstages.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/stages && /usr/bin/cmake -P CMakeFiles/stages.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/construction.cpp.o CMakeFiles/stages.dir/simplification.cpp.o CMakeFiles/stages.dir/ss_edge_split.cpp.o /usr/bin/ranlib libstages.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 72%] Built target stages make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/utils /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/CMakeFiles/utils.dir/depend.internal". 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Scanning dependencies of target utils make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 73%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/memory_limit.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/memory_limit.cpp [ 73%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp [ 73%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp [ 75%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/temporary.cpp [ 75%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/common/utils -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger_impl.cpp [ 76%] Linking CXX static library libutils.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/logger/logger_impl.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target utils make -f common/utils/kmer_mph/CMakeFiles/mph_index.dir/build.make common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph/CMakeFiles/mph_index.dir/depend.internal". Scanning dependencies of target mph_index make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/utils/kmer_mph/CMakeFiles/mph_index.dir/build.make common/utils/kmer_mph/CMakeFiles/mph_index.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Building CXX object common/utils/kmer_mph/CMakeFiles/mph_index.dir/1.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph -I/build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/mph_index.dir/1.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/1.cpp [ 76%] Linking CXX static library libmph_index.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph && /usr/bin/cmake -P CMakeFiles/mph_index.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/utils/kmer_mph && /usr/bin/cmake -E cmake_link_script CMakeFiles/mph_index.dir/link.txt --verbose=1 /usr/bin/ar qc libmph_index.a CMakeFiles/mph_index.dir/1.cpp.o /usr/bin/ranlib libmph_index.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target mph_index make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common /build/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/CMakeFiles/common_modules.dir/depend.internal". Scanning dependencies of target common_modules make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/CMakeFiles/common_modules.dir/build.make common/CMakeFiles/common_modules.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Building CXX object common/CMakeFiles/common_modules.dir/empty.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common -I/build/spades-3.13.1+dfsg/assembler/src/common -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/common_modules.dir/empty.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/empty.cpp [ 76%] Linking CXX static library libcommon_modules.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common && /usr/bin/cmake -P CMakeFiles/common_modules.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/empty.cpp.o /usr/bin/ranlib libcommon_modules.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target common_modules make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/common/io/graph /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph/CMakeFiles/graphio.dir/depend.internal". Scanning dependencies of target graphio make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/graph/gfa_reader.cpp [ 77%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/graph/gfa_writer.cpp [ 77%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/common/io/graph -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/common/io/graph/fastg_writer.cpp [ 77%] Linking CXX static library libgraphio.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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/spades-3.13.1+dfsg/assembler/build_spades' [ 77%] Built target graphio make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/spades /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-stages.dir/depend.internal". Scanning dependencies of target spades-stages make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 77%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/gap_closer.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 77%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp: In instantiation of 'void debruijn_graph::mismatches::MismatchStatistics::Count(io::ReadStream&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; read_type = io::SingleReadSeq; EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:185:32: required from 'void debruijn_graph::mismatches::MismatchStatistics::ParallelCount(SingleStreamList&, const conj_graph_pack&) [with SingleStreamList = io::ReadStreamList; EdgeId = restricted::pure_pointer >; debruijn_graph::conj_graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:304:33: required from 'size_t debruijn_graph::mismatches::MismatchShallNotPass::ParallelStopMismatchIteration(SingleReadStreamList&) [with SingleReadStreamList = io::ReadStreamList; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:335:56: required from 'size_t debruijn_graph::mismatches::MismatchShallNotPass::ParallelStopAllMismatches(SingleReadStreamList&, size_t) [with SingleReadStreamList = io::ReadStreamList; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:26:60: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:150:26: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 150 | MappingRange mr = path[0].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/mismatch_shall_not_pass.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/mismatch_correction.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp: In member function 'void debruijn_graph::InsertSizeCounter::ProcessPairedRead(size_t, const omnigraph::MappingPath > >&, const omnigraph::MappingPath > >&, int, int)': /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:96:49: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | auto mapping_edge_1 = read1.front().second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:97:49: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | auto mapping_edge_2 = read2.front().second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp: In member function 'void debruijn_graph::SSBinCoverageFiller::ProcessRange(size_t, const omnigraph::MappingPath > >&)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:45: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 73 | auto range = read.mapping_at(i).mapped_range; | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:74:81: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 74 | tmp_storages_[thread_index].IncreaseKmerCount(read.edge_at(i), range); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:28, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage.hpp:241:44: note: initializing argument 2 of 'void debruijn_graph::SSCoverageSplitter::IncreaseKmerCount(debruijn_graph::EdgeId, Range)' 241 | void IncreaseKmerCount(EdgeId e, Range mapped_range) { | ~~~~~~^~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::CollectLibInformation(const conj_graph_pack&, size_t&, size_t, size_t)': /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:224:46: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 224 | if (data.median_insert_size < gp.k_value + 2) | ~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::MappingPath::mapping_at(size_t) const [with ElementId = restricted::pure_pointer >; size_t = long unsigned int]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/rna/ss_coverage_filler.hpp:73:43: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:236:35: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 236 | return range_mappings_[idx]; | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp: In instantiation of 'size_t debruijn_graph::stats::Nx(Graph&, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]': /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:319:109: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:457:24: warning: conversion from '__gnu_cxx::__alloc_traits, long unsigned int>::value_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 457 | if (lengths[i] >= len_perc) In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:135, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/math/xmath.h: In instantiation of 'bool math::ls(T, U) [with T = int; U = omnigraph::de::DEWeight]': /build/spades-3.13.1+dfsg/assembler/src/common/math/xmath.h:314:34: required from 'bool math::gr(T, U) [with T = omnigraph::de::DEWeight; U = int]' /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_filler.hpp:75:39: required from here /build/spades-3.13.1+dfsg/assembler/src/common/math/xmath.h:303:17: warning: conversion from 'int' to 'float' may change value [-Wconversion] 303 | return (lhs < rhs); | ^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/memory:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/standard_base.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/insert_size_refiner.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/is_counter.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/pair_info_count.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/io/dataset_support/dataset_readers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:7: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:12: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 78%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/distance_estimation.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp: In constructor 'debruijn_graph::OverlapInfo::OverlapInfo(const Range&, const Range&, size_t)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:7, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp: In member function 'size_t path_extend::OverlapRemover::AnalyzeOverlaps(const path_extend::BidirectionalPath&, const path_extend::BidirectionalPath&, bool, bool) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:53:39: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 53 | auto other_range = range_pair.second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::GetUniqueEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, const string&) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/genome_consistance_checker.hpp:192:115: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:97:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 97 | return *poss.begin(); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/perf/perfcounter.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp: In constructor 'debruijn_graph::OverlapInfo::OverlapInfo(const Range&, const Range&, size_t)': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/overlap_analysis.hpp:17:35: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 17 | match_cnt(match_cnt_) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp: In member function 'size_t path_extend::OverlapRemover::AnalyzeOverlaps(const path_extend::BidirectionalPath&, const path_extend::BidirectionalPath&, bool, bool) const': /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:53:39: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 53 | auto other_range = range_pair.second; | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/paired_library.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/weight_counter.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/extension_chooser.hpp:22, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/path_extender.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/contig_output_stage.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 79%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp: In instantiation of 'pacbio::PacBioMappingIndex::ClustersSet pacbio::PacBioMappingIndex::GetBWAClusters(const Sequence&) const [with Graph = debruijn_graph::DeBruijnGraph; pacbio::PacBioMappingIndex::ClustersSet = std::set, std::less >, std::allocator > >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:411:37: required from 'pacbio::OneReadMapping pacbio::PacBioMappingIndex::GetReadAlignment(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:135:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 135 | omnigraph::MappingRange mr = e_mr.second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::MappingPath::mapping_at(size_t) const [with ElementId = restricted::pure_pointer >; size_t = long unsigned int]': /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:47:54: required from 'std::vector > debruijn_graph::gap_closing::GapTrackingListener::InferGaps(const ReadT&, const omnigraph::MappingPath > >&) const [with ReadT = io::SingleRead]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:69:44: required from 'void debruijn_graph::gap_closing::GapTrackingListener::InnerProcessRead(size_t, const ReadT&, const omnigraph::MappingPath > >&) [with ReadT = io::SingleRead; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:112:53: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:236:35: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 236 | return range_mappings_[idx]; | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp: In instantiation of 'omnigraph::GapDescription omnigraph::CreateGapInfoTryFixOverlap(const Graph&, const ReadT&, size_t, size_t, typename Graph::EdgeId, size_t, typename Graph::EdgeId, size_t) [with Graph = debruijn_graph::DeBruijnGraph; ReadT = io::SingleRead; size_t = long unsigned int; typename Graph::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:53:54: required from 'std::vector > debruijn_graph::gap_closing::GapTrackingListener::InferGaps(const ReadT&, const omnigraph::MappingPath > >&) const [with ReadT = io::SingleRead]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:69:44: required from 'void debruijn_graph::gap_closing::GapTrackingListener::InnerProcessRead(size_t, const ReadT&, const omnigraph::MappingPath > >&) [with ReadT = io::SingleRead; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:112:53: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:5: note: in expansion of macro 'VERIFY' 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:13: note: in expansion of macro 'VERIFY' 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp: In instantiation of 'omnigraph::GapDescription omnigraph::CreateGapInfoTryFixOverlap(const Graph&, const ReadT&, size_t, size_t, typename Graph::EdgeId, size_t, typename Graph::EdgeId, size_t) [with Graph = debruijn_graph::DeBruijnGraph; ReadT = io::SingleReadSeq; size_t = long unsigned int; typename Graph::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:53:54: required from 'std::vector > debruijn_graph::gap_closing::GapTrackingListener::InferGaps(const ReadT&, const omnigraph::MappingPath > >&) const [with ReadT = io::SingleReadSeq]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:69:44: required from 'void debruijn_graph::gap_closing::GapTrackingListener::InnerProcessRead(size_t, const ReadT&, const omnigraph::MappingPath > >&) [with ReadT = io::SingleReadSeq; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:118:53: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:5: note: in expansion of macro 'VERIFY' 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:13: note: in expansion of macro 'VERIFY' 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp: In instantiation of 'omnigraph::MappingPath pacbio::PacBioMappingIndex::FilterSpuriousAlignments(omnigraph::MappingPath, size_t) const [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; size_t = long unsigned int]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:129:54: required from 'pacbio::PacBioMappingIndex::ClustersSet pacbio::PacBioMappingIndex::GetBWAClusters(const Sequence&) const [with Graph = debruijn_graph::DeBruijnGraph; pacbio::PacBioMappingIndex::ClustersSet = std::set, std::less >, std::allocator > >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:411:37: required from 'pacbio::OneReadMapping pacbio::PacBioMappingIndex::GetReadAlignment(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:92:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 92 | omnigraph::MappingRange current = mapped_path[i].second; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:106:30: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 106 | res.push_back(mapped_path[i].first, mapped_path[i].second); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:280:47: note: initializing argument 2 of 'void omnigraph::MappingPath::push_back(ElementId, omnigraph::MappingRange) [with ElementId = restricted::pure_pointer >]' 280 | void push_back(ElementId id, MappingRange range) { | ~~~~~~~~~~~~~^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:114:41: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 114 | omnigraph::MappingRange mr = e_mr.second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp: In instantiation of 'omnigraph::GapDescription omnigraph::CreateGapInfoTryFixOverlap(const Graph&, const ReadT&, size_t, size_t, typename Graph::EdgeId, size_t, typename Graph::EdgeId, size_t) [with Graph = debruijn_graph::DeBruijnGraph; ReadT = Sequence; size_t = long unsigned int; typename Graph::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:347:62: required from 'pacbio::OneReadMapping pacbio::PacBioMappingIndex::AddGapDescriptions(const std::vector >::iterator>&, const std::vector >::iterator>&, const std::vector >&, const Sequence&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph; typename std::set >::iterator = std::_Rb_tree, pacbio::KmerCluster, std::_Identity >, std::less >, std::allocator > >::const_iterator; typename Graph::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:439:16: required from 'pacbio::OneReadMapping pacbio::PacBioMappingIndex::GetReadAlignment(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:206:77: required from here /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:44: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:183:5: note: in expansion of macro 'VERIFY' 183 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:20:15: note: in definition of macro 'VERIFY' 20 | if (!(expr)) \ | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree.h:103, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.13.1+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:52: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/gap_info.hpp:214:13: note: in expansion of macro 'VERIFY' 214 | VERIFY(left_offset > 0 && right_offset >= 0 && | ^~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/long_read_mapper.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:15, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp: In function 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = omnigraph::GapDescription]': /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:126:67: warning: '*((void*)(& __tmp)+64).Sequence::from_' may be used uninitialized in this function [-Wmaybe-uninitialized] 126 | : from_(from), size_(size), rtl_(rtl), data_(seq.data_) {} | ^ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)(& __tmp)+64).Sequence::from_' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:126:67: warning: '*((void*)(& __tmp)+64).Sequence::size_' may be used uninitialized in this function [-Wmaybe-uninitialized] 126 | : from_(from), size_(size), rtl_(rtl), data_(seq.data_) {} | ^ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)(& __tmp)+64).Sequence::size_' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:168:47: warning: '*((void*)& __tmp +80)' may be used uninitialized in this function [-Wmaybe-uninitialized] 168 | : Sequence(s, s.from_, s.size_, s.rtl_) {} | ~~^~~~ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)& __tmp +80)' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:176:20: warning: '*((void*)& __tmp +80)' may be used uninitialized in this function [-Wmaybe-uninitialized] 176 | rtl_ = rhs.rtl_; | ~~~~^~~~ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)& __tmp +80)' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:175:15: warning: '*((void*)(& __tmp)+64).Sequence::size_' may be used uninitialized in this function [-Wmaybe-uninitialized] 175 | size_ = rhs.size_; | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)(& __tmp)+64).Sequence::size_' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/sequence.hpp:174:15: warning: '*((void*)(& __tmp)+64).Sequence::from_' may be used uninitialized in this function [-Wmaybe-uninitialized] 174 | from_ = rhs.from_; | ~~~~~~^~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_pair.h:59, from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/vector:60, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/values.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/storing_traits.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/pacbio/pac_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:8: /usr/include/c++/10/bits/move.h:197:11: note: '*((void*)(& __tmp)+64).Sequence::from_' was declared here 197 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ [ 80%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/ios:42, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/stacktrace.hpp:17, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/verify.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/stl_utils.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/statistics.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/graph_support/contig_output.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/chromosome_removal.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [ 80%] Linking CXX static library libspades-stages.a cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/spades-3.13.1+dfsg/assembler/build_spades/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 /usr/bin/ranlib libspades-stages.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 80%] Built target spades-stages make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/spades /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades/CMakeFiles/spades-core.dir/depend.internal". Scanning dependencies of target spades-core make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 80%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:181:43: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:183:25: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:141:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 141 | AddEdgePosition(edge, it->contigId, it->mr); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:119:70: note: initializing argument 3 of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' 119 | void AddEdgePosition(EdgeId edge, string contig_id, MappingRange new_pos) { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:181:43: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/launch.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:15: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/path_helper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/main.cpp:11: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/spades/series_analysis.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ [ 82%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/projects/spades -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp: In instantiation of 'bool utils::kmer_index_traits::raw_equal_to::operator()(const Seq&, utils::kmer_index_traits::KMerRawReference) [with Seq = RuntimeSeq<128>; utils::kmer_index_traits::KMerRawReference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:312:54: required from 'bool utils::KeyStoringMap::valid(const KeyWithHash&) const [with K = RuntimeSeq<128>; V = long unsigned int; traits = utils::kmer_index_traits >; StoringType = utils::InvertableStoring; utils::KeyStoringMap::KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:214:25: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:26:60: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 26 | return (adt::array_equal_to()(lhs.data(), lhs.data_size(), rhs)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.hpp:3, from /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:1: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:678:65: note: initializing argument 3 of 'bool adt::array_equal_to::operator()(const ElTy*, size_t, adt::array_equal_to::reference) const [with ElTy = long unsigned int; size_t = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]' 678 | bool operator()(const ElTy *lhs, size_t sz, const reference rhs) const { | ~~~~~~~~~~~~~~~~^~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(const ElTy*, size_t, adt::array_equal_to::reference) const [with ElTy = long unsigned int; size_t = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:26:60: required from 'bool utils::kmer_index_traits::raw_equal_to::operator()(const Seq&, utils::kmer_index_traits::KMerRawReference) [with Seq = RuntimeSeq<128>; utils::kmer_index_traits::KMerRawReference = adt::array_reference >]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:312:54: required from 'bool utils::KeyStoringMap::valid(const KeyWithHash&) const [with K = RuntimeSeq<128>; V = long unsigned int; traits = utils::kmer_index_traits >; StoringType = utils::InvertableStoring; utils::KeyStoringMap::KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' /build/spades-3.13.1+dfsg/assembler/src/projects/mts/contig_abundance.cpp:214:25: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:679:41: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 679 | return const_reference(lhs, sz) == rhs; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:350:48: note: initializing argument 1 of 'bool adt::array_const_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 350 | bool operator==(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 82%] Linking CXX executable ../../bin/spades-core cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-core.dir/main.cpp.o CMakeFiles/spades-core.dir/series_analysis.cpp.o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a -lnlopt ../../ext/bamtools/api/libBamTools.a -lssw ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/assembly_graph/libassembly_graph.a -lhat-trie ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 82%] Built target spades-core make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/hammer /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer/CMakeFiles/spades-hammer.dir/depend.internal". Scanning dependencies of target spades-hammer make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 82%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/main.cpp [ 83%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/hammer_tools.cpp [ 83%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/hamcluster.cpp [ 83%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:356:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 356 | for (uint32_t j=0; j::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = Seq<21>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = Seq<21>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:133:34: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = Seq<21>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/kmer_data.cpp:102:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 84%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp [ 84%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/read_corrector.cpp [ 85%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/hammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/hammer/expander.cpp [ 85%] Linking CXX executable ../../bin/spades-hammer cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic 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 -o ../../bin/spades-hammer ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../common/pipeline/libpipeline.a ../../ext/bamtools/api/libBamTools.a ../../ext/cppformat/libformat.a ../../ext/gqf/libgqf.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/cityhash/libcityhash.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 85%] Built target spades-hammer make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend.internal". Scanning dependencies of target spades-ionhammer make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 85%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_traits.hpp:8, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = hammer::HomopolymerRun; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = hammer::HSeq<16>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = hammer::HomopolymerRun; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = hammer::HSeq<16>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = hammer::HomopolymerRun; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:133:34: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = hammer::HSeq<16>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:80:22: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp:147:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 147 | idx = std::min(idx, (const int)(alphas_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp:131:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 131 | bin = std::min(bin, (const int)(borders_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/config_struct.cpp [ 88%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp [ 88%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const string&, const string&, float&, float&, int)': /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': /build/spades-3.13.1+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; | ~~~~~~~~~~^~ [ 88%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const': /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::Solve(BasecallerRead&, int, int)': /build/spades-3.13.1+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/spades-3.13.1+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/spades-3.13.1+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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp:43, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp:147:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 147 | idx = std::min(idx, (const int)(alphas_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp:44, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'std::vector hammer::correction::HRunSizeSearcher::TryFindAllDeletions(char, bool)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h:383:24: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 383 | const char start = (const char)std::max(1, observed_size_ - max_error_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'hammer::correction::IonEvent hammer::correction::HRunSizeSearcher::TryFindInsertion(char)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h:408:22: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 408 | (const char)(found ? hkmer_[K - 1].len : observed_size_ + 1), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h: In member function 'hammer::correction::IonEvent hammer::correction::HRunSizeSearcher::TryFindDeletion(char)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h:416:24: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 416 | const char start = (const char)std::max(1, observed_size_ - max_error_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/read_corrector_structs_new.h:426:22: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 426 | (const char)(found ? hkmer_[K - 1].len : observed_size_ - 1), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:26: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp: In member function 'void hammer::correction::GammaPoissonLikelihoodCalcer::Update(hammer::correction::GammaPoissonLikelihoodCalcer::PenaltyState&, const hammer::correction::IonEvent&, const hammer::KMerStat*) const': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/penalty_estimator.hpp:160:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 160 | min((const uint)std::abs(event.fixed_size_ - event.overserved_size_), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/main.cpp:28: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp:131:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 131 | bin = std::min(bin, (const int)(borders_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/reference.cpp [ 89%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:18, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp:147:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 147 | idx = std::min(idx, (const int)(alphas_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/subcluster.hpp:19, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.h:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp:131:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 131 | bin = std::min(bin, (const int)(borders_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp [ 90%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp: In member function 'double n_gamma_poisson_model::ParametricClusterModel::ErrorRate(int) const': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.hpp:147:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 147 | idx = std::min(idx, (const int)(alphas_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp:5: /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp: In member function 'double n_normal_model::Binarizer::GetBorder(int)': /build/spades-3.13.1+dfsg/assembler/src/projects/ionhammer/normal_quality_model.hpp:131:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] 131 | bin = std::min(bin, (const int)(borders_.size() - 1)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable ../../bin/spades-ionhammer cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/ionhammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-ionhammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic 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 -o ../../bin/spades-ionhammer ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/bamtools/api/libBamTools.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../ext/cityhash/libcityhash.a make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 91%] Built target spades-ionhammer make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/corrector /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector/CMakeFiles/spades-corrector-core.dir/depend.internal". Scanning dependencies of target spades-corrector-core make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/positional_read.cpp [ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp [ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/contig_processor.cpp /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/contig_processor.cpp:165:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 165 | 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/spades-3.13.1+dfsg/assembler/src/projects/corrector/contig_processor.cpp:165:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 165 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ [ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/dataset_processor.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/config_struct.cpp [ 94%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/projects/corrector -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/corrector/main.cpp [ 94%] Linking CXX executable ../../bin/spades-corrector-core cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic 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 -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 94%] Built target spades-corrector-core make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction /build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend.internal". Scanning dependencies of target spades-truseq-scfcorrection make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 95%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction -I/build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:181:43: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:183:25: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:141:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 141 | AddEdgePosition(edge, it->contigId, it->mr); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:119:70: note: initializing argument 3 of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' 119 | void AddEdgePosition(EdgeId edge, string contig_id, MappingRange new_pos) { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:132:32: required from 'void omnigraph::EdgesPositionHandler::AddAndShiftEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, const std::map, std::set >&, int) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:203:17: required from 'void omnigraph::EdgesPositionHandler::HandleMerge(const std::vector&, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = restricted::pure_pointer >; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:199:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:181:43: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/stage.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/scaffold_correction.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:17: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/string:41, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/filesystem/path_helper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/scaffold_correction/main.cpp:10: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable ../../bin/spades-truseq-scfcorrection cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 95%] Built target spades-truseq-scfcorrection make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-read-filter.dir/depend.internal". Scanning dependencies of target spades-read-filter make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 95%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount -I/build/spades-3.13.1+dfsg/assembler/src/projects/kmercount -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/read_filter.cpp [ 96%] Linking CXX executable ../../bin/spades-read-filter cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 96%] Built target spades-read-filter make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount/CMakeFiles/spades-kmercount.dir/depend.internal". Scanning dependencies of target spades-kmercount make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 97%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount -I/build/spades-3.13.1+dfsg/assembler/src/projects/kmercount -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:132:25: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_splitters.hpp:133:34: required from 'void utils::KMerSortingSplitter::DumpBuffers(const typename utils::KMerSplitter::RawKMers&) [with Seq = RuntimeSeq<128>; typename utils::KMerSplitter::RawKMers = std::vector >]' /build/spades-3.13.1+dfsg/assembler/src/projects/kmercount/main.cpp:99:32: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 97%] Linking CXX executable ../../bin/spades-kmercount cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-kmercount.dir/main.cpp.o -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 97%] Built target spades-kmercount make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend.internal". Scanning dependencies of target spades-gbuilder make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder -I/build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:209:57: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 209 | TRACE("Added to queue " << start_edges.back() << " " << mask); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:125:26: note: in definition of macro 'LOG_MSG' 125 | __logger__str__ << msg; /* don't use brackets here! */ \ | ^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:209:13: note: in expansion of macro 'TRACE' 209 | TRACE("Added to queue " << start_edges.back() << " " << mask); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:213:57: note: initializing argument 2 of 'stream& utils::operator<<(stream&, utils::AbstractDeEdge) [with stream = std::basic_ostream; KWH = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 213 | stream &operator<<(stream &s, const AbstractDeEdge de_edge) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdges(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, std::vector, utils::KMerIndex > > > > >&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:219:61: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 219 | AddStartDeEdgesForVertex(kh, extensions, start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:202:47: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const' 202 | void AddStartDeEdgesForVertex(KeyWithHash kh, utils::InOutMask mask, | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:223:49: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 223 | start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:202:47: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdgesForVertex(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, utils::InOutMask, std::vector, utils::KMerIndex > > > > >&) const' 202 | void AddStartDeEdgesForVertex(KeyWithHash kh, utils::InOutMask mask, | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'bool debruijn_graph::UnbranchingPathExtractor::StepRightIfPossible(debruijn_graph::UnbranchingPathExtractor::DeEdge&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 231 | origin_.GetOutgoing(edge.end, mask.GetUniqueOutgoing())); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:194:32: note: initializing argument 1 of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 194 | AbstractDeEdge(KeyWithHash s, KeyWithHash e) | ~~~~~~~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:241:26: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 241 | DeEdge initial = edge; | ^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'std::vector debruijn_graph::UnbranchingPathExtractor::ConstructLoopFromVertex(const KeyWithHash&, SequenceBuilder&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:257:61: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 257 | DeEdge break_point(kh, origin_.GetUniqueOutgoing(kh)); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:194:32: note: initializing argument 1 of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 194 | AbstractDeEdge(KeyWithHash s, KeyWithHash e) | ~~~~~~~~~~~~^ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:258:68: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 258 | Sequence s = ConstructSequenceWithEdge(break_point, builder); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:237:47: note: initializing argument 1 of 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const' 237 | Sequence ConstructSequenceWithEdge(DeEdge edge, SequenceBuilder &builder) const { | ~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'void debruijn_graph::UnbranchingPathExtractor::CalculateSequences(debruijn_graph::UnbranchingPathExtractor::kmer_iterator&, std::vector&) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:276:44: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 276 | AddStartDeEdges(kh, start_edges); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:213:38: note: initializing argument 1 of 'void debruijn_graph::UnbranchingPathExtractor::AddStartDeEdges(debruijn_graph::UnbranchingPathExtractor::KeyWithHash, std::vector, utils::KMerIndex > > > > >&) const' 213 | void AddStartDeEdges(KeyWithHash kh, std::vector& start_edges) const { | ~~~~~~~~~~~~^~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:278:30: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 278 | for (auto edge : start_edges) { | ^~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:279:69: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 279 | Sequence s = ConstructSequenceWithEdge(edge, builder); | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:237:47: note: initializing argument 1 of 'Sequence debruijn_graph::UnbranchingPathExtractor::ConstructSequenceWithEdge(debruijn_graph::UnbranchingPathExtractor::DeEdge, SequenceBuilder&) const' 237 | Sequence ConstructSequenceWithEdge(DeEdge edge, SequenceBuilder &builder) const { | ~~~~~~~^~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/log_writers.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:8: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:284:34: warning: implicitly-declared 'constexpr utils::AbstractDeEdge, utils::KMerIndex > > > >::AbstractDeEdge(const utils::AbstractDeEdge, utils::KMerIndex > > > >&)' is deprecated [-Wdeprecated-copy] 284 | TRACE("From " << edge << " calculated sequence\n" << s); | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/logger/logger.hpp:125:26: note: in definition of macro 'LOG_MSG' 125 | __logger__str__ << msg; /* don't use brackets here! */ \ | ^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:284:17: note: in expansion of macro 'TRACE' 284 | TRACE("From " << edge << " calculated sequence\n" << s); | ^~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:197:34: note: because 'utils::AbstractDeEdge, utils::KMerIndex > > > >' has user-provided 'utils::AbstractDeEdge& utils::AbstractDeEdge::operator=(const utils::AbstractDeEdge&) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 197 | AbstractDeEdge &operator=(const AbstractDeEdge &that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:213:57: note: initializing argument 2 of 'stream& utils::operator<<(stream&, utils::AbstractDeEdge) [with stream = std::basic_ostream; KWH = utils::InvertableKeyWithHash, utils::KMerIndex > > >]' 213 | stream &operator<<(stream &s, const AbstractDeEdge de_edge) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In member function 'const std::vector debruijn_graph::UnbranchingPathExtractor::CollectLoops(unsigned int)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:319:35: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 319 | if (!IsJunction(kh)) | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:194:33: note: initializing argument 1 of 'bool debruijn_graph::UnbranchingPathExtractor::IsJunction(debruijn_graph::UnbranchingPathExtractor::KeyWithHash) const' 194 | bool IsJunction(KeyWithHash kwh) const { | ~~~~~~~~~~~~^~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:328:35: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 328 | if (IsJunction(kwh)) | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:21: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:194:33: note: initializing argument 1 of 'bool debruijn_graph::UnbranchingPathExtractor::IsJunction(debruijn_graph::UnbranchingPathExtractor::KeyWithHash) const' 194 | bool IsJunction(KeyWithHash kwh) const { | ~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:20, from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:22: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp: In instantiation of 'utils::AbstractDeEdge::AbstractDeEdge(KeyWithHash, KeyWithHash) [with KeyWithHash = utils::InvertableKeyWithHash, utils::KMerIndex > > >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:231:82: required from here /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:195:52: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 195 | : start(std::move(s)), end(std::move(e)) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:195:52: warning: implicitly-declared 'constexpr utils::InvertableKeyWithHash, utils::KMerIndex > > >::InvertableKeyWithHash(const utils::InvertableKeyWithHash, utils::KMerIndex > > >&)' is deprecated [-Wdeprecated-copy] 195 | : start(std::move(s)), end(std::move(e)) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/key_with_hash.hpp:158:28: note: because 'utils::InvertableKeyWithHash, utils::KMerIndex > > >' has user-provided 'utils::InvertableKeyWithHash& utils::InvertableKeyWithHash::operator=(const utils::InvertableKeyWithHash&) [with Key = RuntimeSeq<128>; HashFunction = utils::KMerIndex > >]' 158 | InvertableKeyWithHash &operator=(const InvertableKeyWithHash &that) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/mmapped_reader.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/io/kmers/kmer_iterator.hpp:4, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/ph_map/perfect_hash_map.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:9, from /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:10: /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(adt::array_less::reference, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:363:23: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:261:19: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:75:25: required from 'void utils::DeBruijnExtensionIndexBuilder::BuildExtensionIndexFromStream(fs::TmpDir, Index&, Streams&, io::SingleStream*, size_t) const [with Index = utils::DeBruijnExtensionIndex<>; Streams = io::ReadStreamList; fs::TmpDir = llvm::IntrusiveRefCntPtr; io::SingleStream = io::ReadStream; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:648:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 648 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:244:42: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 244 | bool operator<(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_less::operator()(const value&, adt::array_less::reference) const [with ElTy = long unsigned int; adt::array_less::value = adt::array >; adt::array_less::reference = adt::array_reference >]': /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:248:46: required from 'void libcxx::__insertion_sort_3(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:378:49: required from 'void libcxx::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _Compare = adt::array_less&; _RandomAccessIterator = adt::array_vector_iterator, false>]' /build/spades-3.13.1+dfsg/assembler/ext/include/libcxx/sort.hpp:544:30: required from 'void libcxx::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = adt::array_vector_iterator, false>; _Compare = adt::array_less]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:261:19: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:75:25: required from 'void utils::DeBruijnExtensionIndexBuilder::BuildExtensionIndexFromStream(fs::TmpDir, Index&, Streams&, io::SingleStream*, size_t) const [with Index = utils::DeBruijnExtensionIndex<>; Streams = io::ReadStreamList; fs::TmpDir = llvm::IntrusiveRefCntPtr; io::SingleStream = io::ReadStream; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:640:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 640 | return lhs < rhs; | ~~~~^~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:125:47: note: initializing argument 1 of 'bool adt::array<_Cp>::operator<(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 125 | bool operator<(const array_reference<_Cp> that) const { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp: In instantiation of 'bool adt::array_equal_to::operator()(adt::array_equal_to::reference, adt::array_equal_to::reference) const [with ElTy = long unsigned int; adt::array_equal_to::reference = adt::array_reference >]': /usr/include/c++/10/bits/predefined_ops.h:156:30: required from 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = adt::array_vector_iterator, false>; _Iterator2 = adt::array_vector_iterator, false>; _Compare = adt::array_equal_to]' /usr/include/c++/10/bits/stl_algo.h:951:20: required from '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = adt::array_vector_iterator, false>; _BinaryPredicate = __gnu_cxx::__ops::_Iter_comp_iter >]' /usr/include/c++/10/bits/stl_algo.h:1015:27: required from '_FIter std::unique(_FIter, _FIter, _BinaryPredicate) [with _FIter = adt::array_vector_iterator, false>; _BinaryPredicate = adt::array_equal_to]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:265:28: required from 'size_t utils::KMerDiskCounter::MergeKMers(const string&, const string&) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:124:16: required from 'size_t utils::KMerDiskCounter::Count(unsigned int, unsigned int) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/kmer_mph/kmer_index_builder.hpp:162:20: required from 'size_t utils::KMerDiskCounter::CountAll(unsigned int, unsigned int, bool) [with Seq = RuntimeSeq<128>; traits = utils::kmer_index_traits >; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/utils/extension_index/kmer_extension_index_builder.hpp:75:25: required from 'void utils::DeBruijnExtensionIndexBuilder::BuildExtensionIndexFromStream(fs::TmpDir, Index&, Streams&, io::SingleStream*, size_t) const [with Index = utils::DeBruijnExtensionIndex<>; Streams = io::ReadStreamList; fs::TmpDir = llvm::IntrusiveRefCntPtr; io::SingleStream = io::ReadStream; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/projects/gbuilder/main.cpp:151:121: required from here /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:675:20: warning: implicitly-declared 'constexpr adt::array_reference >::array_reference(const adt::array_reference >&)' is deprecated [-Wdeprecated-copy] 675 | return lhs == rhs; | ~~~~^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:225:22: note: because 'adt::array_reference >' has user-provided 'adt::array_reference<_Cp>& adt::array_reference<_Cp>::operator=(adt::array_reference<_Cp>) [with _Cp = adt::array_vector]' 225 | array_reference &operator=(const array_reference that) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/adt/array_vector.hpp:266:43: note: initializing argument 1 of 'bool adt::array_reference<_Cp>::operator==(adt::array_reference<_Cp>) const [with _Cp = adt::array_vector]' 266 | bool operator==(const array_reference that) const { | ~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 98%] Linking CXX executable ../../bin/spades-gbuilder cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-gbuilder.dir/main.cpp.o -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Built target spades-gbuilder make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' cd /build/spades-3.13.1+dfsg/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.13.1+dfsg/assembler/src /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper /build/spades-3.13.1+dfsg/assembler/build_spades /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/depend.internal". Dependee "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper/CMakeFiles/spades-gmapper.dir/depend.internal". Scanning dependencies of target spades-gmapper make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper -I/build/spades-3.13.1+dfsg/assembler/src/projects/gmapper -I/build/spades-3.13.1+dfsg/assembler/src/include -I/build/spades-3.13.1+dfsg/assembler/build_spades/include -I/build/spades-3.13.1+dfsg/assembler/src -I/build/spades-3.13.1+dfsg/assembler/src/common -isystem /build/spades-3.13.1+dfsg/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In constructor 'omnigraph::MappingRange::MappingRange(Range, Range)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:58:70: warning: implicitly-declared 'constexpr Range::Range(const Range&)' is deprecated [-Wdeprecated-copy] 58 | : initial_range(initial_range), mapped_range(mapped_range) {} | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/sequence/range.hpp:57:12: note: because 'Range' has user-provided 'Range& Range::operator=(const Range&)' 57 | Range& operator=(const Range& other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::ShiftInitial(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:68:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 68 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:70:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 70 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Shift(int) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:77:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 77 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:89:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 89 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::Fit(size_t) const': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:96:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 96 | MappingRange result(*this); | ^ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:105:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 105 | return result; | ^~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:120:17: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 120 | return *this; | ^~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In constructor 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:83: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ^ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 108 | result.push_back(EdgePosition(it->first, *pos_it)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:28:49: note: initializing argument 2 of 'omnigraph::EdgePosition::EdgePosition(std::string, omnigraph::MappingRange)' 28 | EdgePosition(string _contigId, MappingRange _mr) : contigId(_contigId), mr(_mr) { | ~~~~~~~~~~~~~^~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:26, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp: In instantiation of 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]': /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:51:37: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 51 | omnigraph::MappingRange mr = path[i].second; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 124 | new_pos = EraseAndExtract(new_set, new_pos); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:69:74: note: initializing argument 2 of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' 69 | MappingRange EraseAndExtract(set &ranges, MappingRange new_pos) const { | ~~~~~~~~~~~~~^~~~~~~ /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:78:16: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 78 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition]': /usr/include/c++/10/bits/alloc_traits.h:512:17: required from 'static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = omnigraph::EdgePosition; _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; std::allocator_traits >::allocator_type = std::allocator]' /usr/include/c++/10/bits/vector.tcc:115:30: required from 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {omnigraph::EdgePosition}; _Tp = omnigraph::EdgePosition; _Alloc = std::allocator]' /usr/include/c++/10/bits/stl_vector.h:1204:21: required from 'void std::vector<_Tp, _Alloc>::push_back(std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = omnigraph::EdgePosition; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = omnigraph::EdgePosition]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:108:33: required from 'std::vector omnigraph::EdgesPositionHandler::GetEdgePositions(omnigraph::EdgesPositionHandler::EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:290:78: required from 'void debruijn_graph::graphio::DataPrinter::SavePositions(const string&, const omnigraph::EdgesPositionHandler&) const [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graphio.hpp:695:30: required from 'void debruijn_graph::graphio::PrintGraphPack(const string&, debruijn_graph::graphio::DataPrinter&, const graph_pack&) [with graph_pack = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string; typename graph_pack::graph_t = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:299:78: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:25:8: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 25 | struct EdgePosition { | ^~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/10/bits/c++allocator.h:33, from /usr/include/c++/10/bits/allocator.h:46, from /usr/include/c++/10/vector:64, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:7: /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method 'omnigraph::EdgePosition::EdgePosition(omnigraph::EdgePosition&&)' first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, std::set::iterator&, const omnigraph::MappingRange&) const [with Graph = debruijn_graph::DeBruijnGraph; std::set::iterator = std::_Rb_tree, std::less, std::allocator >::const_iterator]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:72:38: required from 'omnigraph::MappingRange omnigraph::EdgesPositionHandler::EraseAndExtract(std::set&, omnigraph::MappingRange) const [with Graph = debruijn_graph::DeBruijnGraph]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:124:34: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:116:24: required from 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, size_t, size_t, size_t, size_t) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string; size_t = long unsigned int]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:66:38: required from 'visualization::position_filler::PosFiller::MappingPath visualization::position_filler::PosFiller::Process(const io::SingleRead&) const [with Graph = debruijn_graph::DeBruijnGraph; visualization::position_filler::PosFiller::MappingPath = omnigraph::MappingPath > >]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:79:20: required from 'void visualization::position_filler::PosFiller::Process(io::SingleStream&) const [with Graph = debruijn_graph::DeBruijnGraph; io::SingleStream = io::ReadStream]' /build/spades-3.13.1+dfsg/assembler/src/common/visualization/position_filler.hpp:92:23: required from 'void visualization::position_filler::FillPos(gp_t&, const string&, std::string, bool) [with gp_t = debruijn_graph::graph_pack; std::string = std::__cxx11::basic_string]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:67:46: required from 'void debruijn_graph::stats::CollectContigPositions(graph_pack&) [with graph_pack = debruijn_graph::graph_pack]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:244:30: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:50:14: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 50 | auto old_pos = *position; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:58:20: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 58 | return new_pos; | ^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp: In instantiation of 'void omnigraph::EdgesPositionHandler::AddEdgePositions(omnigraph::EdgesPositionHandler::EdgeId, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]': /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:183:25: required from 'void omnigraph::EdgesPositionHandler::HandleGlue(omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId, omnigraph::EdgesPositionHandler::EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >]' /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:179:18: required from here /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:141:28: warning: implicitly-declared 'constexpr omnigraph::MappingRange::MappingRange(const omnigraph::MappingRange&)' is deprecated [-Wdeprecated-copy] 141 | AddEdgePosition(edge, it->contigId, it->mr); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/paths/mapping_path.hpp:117:18: note: because 'omnigraph::MappingRange' has user-provided 'omnigraph::MappingRange omnigraph::MappingRange::operator=(const omnigraph::MappingRange&)' 117 | MappingRange operator = (const MappingRange & other) { | ^~~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/visualization/graph_labeler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/id_track_handler.hpp:12, from /build/spades-3.13.1+dfsg/assembler/src/common/pipeline/graph_pack.hpp:13, from /build/spades-3.13.1+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:9: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/handlers/edges_position_handler.hpp:119:70: note: initializing argument 3 of 'void omnigraph::EdgesPositionHandler::AddEdgePosition(omnigraph::EdgesPositionHandler::EdgeId, std::string, omnigraph::MappingRange) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::EdgesPositionHandler::EdgeId = restricted::pure_pointer >; std::string = std::__cxx11::basic_string]' 119 | void AddEdgePosition(EdgeId edge, string contig_id, MappingRange new_pos) { | ~~~~~~~~~~~~~^~~~~~~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:16, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(omnigraph::GraphCore::VertexId, omnigraph::GraphCore::VertexId, const EdgeData&, restricted::IdDistributor&) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': /build/spades-3.13.1+dfsg/assembler/src/common/adt/small_pod_vector.hpp:361:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'restricted::pure_pointer > [1]'} [-Warray-bounds] 361 | ++vptr; | ^~ In file included from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:14, from /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.13.1+dfsg/assembler/src/projects/gmapper/main.cpp:7: /build/spades-3.13.1+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:338:12: note: while referencing 'e' 338 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, const EdgeData &data, | ^~~~~~~~~~~~~ [100%] Linking CXX executable ../../bin/spades-gmapper cd /build/spades-3.13.1+dfsg/assembler/build_spades/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/spades-3.13.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spades-gmapper.dir/main.cpp.o -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../ext/cppformat/libformat.a ../../ext/jemalloc/libjemalloc.a -lz ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a -lz ../../ext/llvm/libllvm-support.a -ldl ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/paired_info/libpaired_info.a ../../common/modules/path_extend/libpath_extend.a ../../common/assembly_graph/libassembly_graph.a -lhat-trie -lssw ../../common/stages/libstages.a ../../ext/gqf/libgqf.a ../../common/utils/libutils.a ../../common/utils/kmer_mph/libmph_index.a ../../ext/cityhash/libcityhash.a ../../common/modules/libmodules.a -lbwa make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' /usr/bin/cmake -E cmake_progress_start /build/spades-3.13.1+dfsg/assembler/build_spades/CMakeFiles 0 make[2]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[2]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[3]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 9%] Built target jemalloc make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 14%] Built target ConsensusCore make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 30%] Built target BamTools make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 38%] Built target samtools make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 39%] Built target format make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 40%] Built target cityhash make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 41%] Built target getopt_pp make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 51%] Built target llvm-support make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 52%] Built target gqf make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target edlib make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 53%] Built target gfa1 make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 54%] Built target coverage_model make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 55%] Built target input make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 58%] Built target pipeline make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 59%] Built target sequence make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 63%] Built target assembly_graph make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 67%] Built target path_extend make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 70%] Built target modules make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 71%] Built target paired_info make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 72%] Built target stages make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target utils make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target mph_index make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 76%] Built target common_modules make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 77%] Built target graphio make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 80%] Built target spades-stages make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 82%] Built target spades-core make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 85%] Built target spades-hammer make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 91%] Built target spades-ionhammer make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 94%] Built target spades-corrector-core make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 95%] Built target spades-truseq-scfcorrection make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 96%] Built target spades-read-filter make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 97%] Built target spades-kmercount make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [ 98%] Built target spades-gbuilder make[4]: Entering directory '/build/spades-3.13.1+dfsg/assembler/build_spades' make[4]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' [100%] Built target spades-gmapper make[3]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' Install the project... -- Install configuration: "RelWithDebInfo" -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/metaspades.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/plasmidspades.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/truspades.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades_init.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/VERSION -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/reference_1K.fa.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.txt -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.gff -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.txt -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.gff -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/manual.html -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/README.md -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/truspades_manual.html -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/rnaspades_manual.html -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/LICENSE -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/GPLv2.txt -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-core -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/tsa.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/toy.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/simplification.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/rna_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/plasmid_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/pe_params.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/moleculo_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/meta_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/mda_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/large_genome_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/distance_estimation.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/detail_info_printer.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/construction.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/config.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mda_mode.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-hammer -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer/config.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-ionhammer -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer/ionhammer.cfg -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-corrector-core -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector/corrector.info -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-truseq-scfcorrection -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-kmercount -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-gbuilder -- Installing: /build/spades-3.13.1+dfsg/install_spades/bin/spades-gmapper -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/hammer_logic.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/process_cfg.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/spades_logic.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/corrector_logic.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/support.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/options_storage.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/id_generation.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/launch_options.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/alignment.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/sam_parser.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/SeqIO.py -- Installing: /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/__init__.py make[2]: Leaving directory '/build/spades-3.13.1+dfsg/assembler/build_spades' find /build/spades-3.13.1+dfsg/install_spades \ -type f \ -print0 \ -exec sed -i 's/pyyaml[2|3]/yaml/' {} + /build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/__init__.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/SeqIO.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/sam_parser.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/common/alignment.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/launch_options.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/id_generation.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/options_storage.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/support.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/corrector_logic.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/spades_logic.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/process_cfg.py/build/spades-3.13.1+dfsg/install_spades/share/spades/spades_pipeline/hammer_logic.py/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/corrector/corrector.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/ionhammer/ionhammer.cfg/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/hammer/config.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mda_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/careful_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/config.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/construction.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/detail_info_printer.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/distance_estimation.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/large_genome_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/mda_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/meta_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/moleculo_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/pe_params.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/plasmid_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/rna_mode.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/simplification.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/toy.info/build/spades-3.13.1+dfsg/install_spades/share/spades/configs/debruijn/tsa.info/build/spades-3.13.1+dfsg/install_spades/share/spades/GPLv2.txt/build/spades-3.13.1+dfsg/install_spades/share/spades/LICENSE/build/spades-3.13.1+dfsg/install_spades/share/spades/rnaspades_manual.html/build/spades-3.13.1+dfsg/install_spades/share/spades/truspades_manual.html/build/spades-3.13.1+dfsg/install_spades/share/spades/README.md/build/spades-3.13.1+dfsg/install_spades/share/spades/manual.html/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl1.fq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_plasmid/pl2.fq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.gff/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/genes_1K.txt/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.gff/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/operons_1K.txt/build/spades-3.13.1+dfsg/install_spades/share/spades/test_dataset/reference_1K.fa.gz/build/spades-3.13.1+dfsg/install_spades/share/spades/VERSION/build/spades-3.13.1+dfsg/install_spades/bin/spades-gmapper/build/spades-3.13.1+dfsg/install_spades/bin/spades-gbuilder/build/spades-3.13.1+dfsg/install_spades/bin/spades-kmercount/build/spades-3.13.1+dfsg/install_spades/bin/spades-truseq-scfcorrection/build/spades-3.13.1+dfsg/install_spades/bin/spades-corrector-core/build/spades-3.13.1+dfsg/install_spades/bin/spades-ionhammer/build/spades-3.13.1+dfsg/install_spades/bin/spades-hammer/build/spades-3.13.1+dfsg/install_spades/bin/spades-core/build/spades-3.13.1+dfsg/install_spades/bin/spades_init.py/build/spades-3.13.1+dfsg/install_spades/bin/truspades.py/build/spades-3.13.1+dfsg/install_spades/bin/spades.pymake[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/spades-3.13.1+dfsg' # Ugly hack to make files available for dh_aut_test and autopkgtest mkdir -p /build/spades-3.13.1+dfsg/../share/ ln -s /build/spades-3.13.1+dfsg/install_spades/share/spades /build/spades-3.13.1+dfsg/../share/ ln -s /usr/bin/bwa /build/spades-3.13.1+dfsg/install_spades/bin/spades-bwa /build/spades-3.13.1+dfsg/install_spades/bin/spades.py --test Command line: /build/spades-3.13.1+dfsg/install_spades/bin/spades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.2 OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset) Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log ===== Read error correction started. == Running read error correction tool: /build/spades-3.13.1+dfsg/install_spades/bin/spades-hammer /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info 0:00:00.001 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.001 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.001 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.001 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.001 4M / 4M INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:03.921 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:04.040 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:04.142 8G / 8G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 0:00:04.682 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.090 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. 0:00:05.090 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.121 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:05.514 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:05.515 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). 0:00:05.515 64M / 8G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:00:05.558 64M / 8G INFO General (main.cpp : 148) Clustering Hamming graph. 0:00:05.674 64M / 8G INFO General (main.cpp : 155) Extracting clusters 0:00:05.742 64M / 8G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 0:00:05.742 64M / 8G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:00:05.742 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:05.838 64M / 8G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:05.942 64M / 8G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:00:05.942 64M / 8G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. 0:00:05.942 64M / 8G INFO General (main.cpp : 173) Subclustering Hamming graph 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 0:00:05.966 64M / 8G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) 0:00:05.966 64M / 8G INFO General (main.cpp : 178) Finished clustering. 0:00:05.966 64M / 8G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:00:06.082 64M / 8G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 0:00:06.082 64M / 8G INFO General (main.cpp : 222) Solid k-mers finalized 0:00:06.082 64M / 8G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:00:06.082 64M / 8G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:06.311 408M / 8G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. 0:00:06.348 408M / 8G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:00:06.353 408M / 8G INFO General (hammer_tools.cpp : 185) Written batch 0 0:00:06.432 64M / 8G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. 0:00:06.432 64M / 8G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. 0:00:06.432 64M / 8G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml 0:00:06.432 64M / 8G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K21/configs/config.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=21 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.135 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.137 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.333 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.334 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.560 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.567 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.567 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.567 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.567 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.568 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.568 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.568 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:04.527 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.069 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.069 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.455 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. 0:00:05.455 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.492 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.492 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.492 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.492 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.492 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:05.492 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:09.055 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. 0:00:09.585 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.935 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. 0:00:09.935 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.963 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.631 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.632 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). 0:00:10.632 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.687 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.687 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.687 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.687 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.763 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper 0:00:10.763 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.763 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.779 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:10.807 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.827 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.887 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.887 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.887 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.267 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). 0:00:11.267 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.339 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.391 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 348 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 348. Coverage mad: 62.2692 0:00:11.392 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:11.591 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:11.877 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:12.328 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:13.025 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:14.162 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:16.925 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 342.845. Fitted coverage std. dev: 68.3997 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.999994 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 355 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 171 0:00:16.927 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 749 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 342.845 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 171 0:00:16.927 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:16.927 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:16.927 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:16.928 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:16.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:16.951 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:16.999 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:16.999 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:17.039 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:17.039 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:17.067 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:17.067 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:17.067 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:17.067 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:17.067 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:17.067 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.099 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.099 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.131 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.131 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.155 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:17.155 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.175 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.175 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.199 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.199 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.227 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.227 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:17.227 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:17.227 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:17.227 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.255 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.255 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.271 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.271 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.319 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.319 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:17.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:17.339 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:17.339 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:17.339 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 0:00:17.339 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:17.339 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta 0:00:17.339 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:17.339 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 17 seconds Max read length detected as 100 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.913 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.575 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.575 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.028 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. 0:00:05.028 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.053 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.053 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.053 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.053 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.053 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:05.053 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.949 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. 0:00:09.550 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.944 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. 0:00:09.944 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.336 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.338 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). 0:00:10.338 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.460 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.460 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.460 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.460 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.572 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper 0:00:10.572 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.572 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.612 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:10.644 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.676 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.744 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.744 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.744 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.156 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). 0:00:11.156 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.244 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.293 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 17 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 17. Coverage mad: 11.8608 0:00:11.293 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:11.390 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:11.565 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:11.757 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:11.936 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:12.274 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:12.967 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 64 0:00:14.437 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 128 0:00:16.275 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 108.181. Fitted coverage std. dev: 65.0594 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 0.0555142 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 3 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 3 0:00:16.277 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 400 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 108.181 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 3 0:00:16.277 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:16.277 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:16.277 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:16.277 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:16.277 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:16.300 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:16.300 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:16.340 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:16.340 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:16.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:16.376 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:16.404 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:16.404 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:16.404 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:16.404 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.404 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:16.404 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.432 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.432 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.472 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:16.472 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.500 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.500 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.512 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.512 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.524 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.524 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:16.524 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:16.524 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.524 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.540 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.540 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.557 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.557 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.580 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.580 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.592 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.592 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:16.592 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:16.604 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:16.604 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:16.604 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 0:00:16.604 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:16.604 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:16.605 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:16.605 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 16 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.672 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.206 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.206 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.624 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:04.624 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.647 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.656 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.656 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.656 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.656 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:04.656 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.401 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. 0:00:08.972 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.324 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:09.324 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.350 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.772 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.772 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). 0:00:09.773 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.850 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.851 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.851 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.884 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted 0:00:09.916 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:09.940 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:09.980 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:09.980 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:09.980 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.312 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:10.312 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.356 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.412 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 0 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 6 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 6. Coverage mad: 4.4478 0:00:10.413 64M / 8G INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:10.489 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:10.533 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:10.652 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:10.833 64M / 8G INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 13.7375. Fitted coverage std. dev: 9.60863 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 2.02732e-07 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 1 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 1 0:00:10.992 64M / 8G INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 238 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 112) Mean coverage was calculated as 13.7375 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 1 0:00:10.992 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:10.992 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:10.992 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:10.992 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.992 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:10.993 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:10.993 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:10.993 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:14.596 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. 0:00:15.125 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:15.472 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:15.472 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:15.499 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:15.800 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:15.801 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:15.801 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:15.848 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:15.848 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:15.848 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:15.884 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:15.884 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:15.884 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:15.884 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates 0:00:15.924 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:15.924 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:15.924 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:15.924 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:15.956 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:15.956 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:15.996 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:15.996 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:16.032 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:16.032 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:16.060 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times 0:00:16.060 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:16.060 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:16.060 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.060 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:16.060 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.088 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:16.088 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.120 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.120 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.152 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:16.152 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.192 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.192 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.216 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.216 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.240 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.240 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:16.240 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:16.240 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:16.240 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:16.240 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:16.240 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:16.240 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:19.956 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:20.519 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:20.896 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:20.896 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:20.926 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:21.320 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:21.320 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:21.321 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:21.368 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:21.369 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:21.369 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:21.438 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:21.438 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:21.438 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:21.438 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:21.488 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:21.488 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:21.488 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:21.488 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:21.532 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:21.532 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:21.584 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:21.584 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:21.624 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:21.624 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:21.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:21.664 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:21.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:21.684 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:21.684 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:21.684 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 0:00:21.684 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:21.684 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:21.684 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:21.718 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:21.718 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:21.718 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:21.718 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:21.718 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:21.718 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:21.719 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:21.719 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta 0:00:21.719 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:21.719 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:21.719 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 945 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:21.719 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:21.932 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:22.811 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:22.916 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:22.916 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:22.919 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 0:00:23.028 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:23.029 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:23.045 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:23.045 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 2, rounding threshold 0 0:00:23.058 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:23.076 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:23.087 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:23.087 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:23.087 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:23.087 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:23.096 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:23.096 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:23.096 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:23.136 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:23.179 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:23.179 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:23.179 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:23.188 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:23.188 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:23.188 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:23.188 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:23.188 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:23.188 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:23.188 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:23.188 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 278) Estimated coverage of library #0 is 140.62 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:23.188 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:23.188 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 0:00:23.188 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:23.188 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:23.188 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:23.188 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:23.188 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:23.188 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:23.188 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:23.188 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:23.188 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:23.188 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:23.188 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 298) Sorting paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:23.188 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:23.188 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:23.188 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:23.188 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:23.188 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:23.188 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:23.188 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:23.189 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:23.189 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:23.189 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 23 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /build/spades-3.13.1+dfsg/spades_test/corrected/ * Assembled contigs are in /build/spades-3.13.1+dfsg/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-3.13.1+dfsg/spades_test/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /build/spades-3.13.1+dfsg/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-3.13.1+dfsg/spades_test/scaffolds.paths * Assembly graph is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log Thank you for using SPAdes! /build/spades-3.13.1+dfsg/install_spades/bin/metaspades.py --test Command line: /build/spades-3.13.1+dfsg/install_spades/bin/metaspades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.2 OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: read error correction and assembling Debug mode is turned OFF Dataset parameters: Metagenomic mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Assembly parameters: k: [21, 33, 55] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log ===== Read error correction started. == Running read error correction tool: /build/spades-3.13.1+dfsg/install_spades/bin/spades-hammer /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 75) Starting BayesHammer, built from N/A, git revision N/A 0:00:00.008 4M / 4M INFO General (main.cpp : 76) Loading config from /build/spades-3.13.1+dfsg/spades_test/corrected/configs/config.info 0:00:00.009 4M / 4M INFO General (main.cpp : 78) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.009 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.009 4M / 4M INFO General (main.cpp : 86) Trying to determine PHRED offset 0:00:00.009 4M / 4M INFO General (main.cpp : 92) Determined value is 33 0:00:00.009 4M / 4M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ] 0:00:00.009 4M / 4M INFO General (main.cpp : 113) Size of aux. kmer data 24 bytes === ITERATION 0 begins === 0:00:00.009 4M / 4M INFO K-mer Counting (kmer_data.cpp : 280) Estimating k-mer count 0:00:00.167 260M / 260M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:00.244 320M / 320M INFO K-mer Counting (kmer_data.cpp : 285) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:00.280 320M / 320M INFO K-mer Counting (kmer_data.cpp : 299) Total 4108 reads processed 0:00:01.095 64M / 320M INFO K-mer Counting (kmer_data.cpp : 311) Filtering singleton k-mers 38 8 0 nslots: 1073741824 bits per slot: 8 range: 0000004000000000 0:00:01.095 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:01.332 1G / 1G INFO K-mer Counting (kmer_data.cpp : 317) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:01.500 1G / 1G INFO K-mer Counting (kmer_data.cpp : 331) Total 4108 reads processed 0:00:01.500 1G / 1G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:01.500 1G / 1G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:01.500 1G / 1G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:01.500 1G / 1G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.951416 Gb 0:00:01.500 1G / 1G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:05.229 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:05.308 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 97) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:05.388 10G / 10G INFO K-mer Splitting (kmer_data.cpp : 112) Total 4108 reads processed 0:00:05.913 1G / 10G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:06.308 1G / 10G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 1974 kmers in total. 0:00:06.308 1G / 10G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:06.344 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:06.892 1G / 10G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:06.893 1G / 10G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 10136 bytes occupied (41.078 bits per kmer). 0:00:06.906 64M / 10G INFO K-mer Counting (kmer_data.cpp : 356) Arranging kmers in hash map order 0:00:06.920 64M / 10G INFO General (main.cpp : 148) Clustering Hamming graph. 0:00:06.972 64M / 10G INFO General (main.cpp : 155) Extracting clusters 0:00:07.012 64M / 10G INFO General (main.cpp : 167) Clustering done. Total clusters: 1960 0:00:07.012 64M / 10G INFO K-mer Counting (kmer_data.cpp : 376) Collecting K-mer information, this takes a while. 0:00:07.012 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_1.fq.gz 0:00:07.100 64M / 10G INFO K-mer Counting (kmer_data.cpp : 382) Processing /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:07.200 64M / 10G INFO K-mer Counting (kmer_data.cpp : 389) Collection done, postprocessing. 0:00:07.200 64M / 10G INFO K-mer Counting (kmer_data.cpp : 402) There are 1974 kmers in total. Among them 0 (0%) are singletons. 0:00:07.200 64M / 10G INFO General (main.cpp : 173) Subclustering Hamming graph 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 649) Subclustering done. Total 0 non-read kmers were generated. 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 650) Subclustering statistics: 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 652) Total singleton subclusters: 8. Among them 8 (100%) are good 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 653) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 654) Average size of non-trivial subcluster: 2.8 kmers 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 655) Average number of sub-clusters per non-singleton cluster: 1.28571 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 656) Total solid k-mers: 1964 0:00:07.220 64M / 10G INFO Hamming Subclustering (kmer_cluster.cpp : 657) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875)) 0:00:07.220 64M / 10G INFO General (main.cpp : 178) Finished clustering. 0:00:07.220 64M / 10G INFO General (main.cpp : 197) Starting solid k-mers expansion in 16 threads. 0:00:07.344 64M / 10G INFO General (main.cpp : 218) Solid k-mers iteration 0 produced 0 new k-mers. 0:00:07.344 64M / 10G INFO General (main.cpp : 222) Solid k-mers finalized 0:00:07.344 64M / 10G INFO General (hammer_tools.cpp : 220) Starting read correction in 16 threads. 0:00:07.344 64M / 10G INFO General (hammer_tools.cpp : 233) Correcting pair of reads: /build/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/share/spades/test_dataset/ecoli_1K_2.fq.gz 0:00:07.567 408M / 10G INFO General (hammer_tools.cpp : 168) Prepared batch 0 of 2054 reads. 0:00:07.586 408M / 10G INFO General (hammer_tools.cpp : 175) Processed batch 0 0:00:07.592 408M / 10G INFO General (hammer_tools.cpp : 185) Written batch 0 0:00:07.672 64M / 10G INFO General (hammer_tools.cpp : 274) Correction done. Changed 4 bases in 4 reads. 0:00:07.672 64M / 10G INFO General (hammer_tools.cpp : 275) Failed to correct 0 bases out of 353915. 0:00:07.672 64M / 10G INFO General (main.cpp : 255) Saving corrected dataset description to /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml 0:00:07.672 64M / 10G INFO General (main.cpp : 262) All done. Exiting. == Compressing corrected reads (with gzip) == Dataset description file was created: /build/spades-3.13.1+dfsg/spades_test/corrected/corrected.yaml ===== Read error correction finished. ===== Assembling started. == Running assembler: K21 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K21/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K21/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K21/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=21 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.130 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.132 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.332 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.333 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.545 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.548 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.548 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.548 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.548 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.549 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.549 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.549 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:04.442 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.035 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.035 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.460 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 984 kmers in total. 0:00:05.460 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.497 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.497 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.497 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.498 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.498 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:05.498 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 262144 0:00:09.216 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 984 kmers. 0:00:09.855 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:10.212 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 985 kmers in total. 0:00:10.212 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:10.232 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.628 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.629 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.399 bits per kmer). 0:00:10.629 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.700 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.701 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.701 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.701 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.772 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 22-mers were removed by early tip clipper 0:00:10.773 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.773 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.788 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:10.820 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.836 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.884 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.884 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.884 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.101 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (79.4797 bits per kmer). 0:00:11.101 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.168 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.216 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:11.216 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:11.216 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:11.216 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:11.247 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:11.247 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:11.279 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:11.279 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:11.308 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:11.308 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:11.352 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:11.352 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:11.352 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:11.353 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:11.353 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:11.353 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.376 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.376 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.401 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.401 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.440 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.440 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.441 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.441 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:11.441 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.459 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.459 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.475 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.475 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.490 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.490 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:11.490 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:11.490 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:11.490 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:11.506 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:11.507 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:11.522 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:11.523 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:11.539 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:11.544 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:11.553 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:11.553 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:11.587 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.603 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.603 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:11.617 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:11.617 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:11.635 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:11.635 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:11.665 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:11.665 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:11.682 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:11.724 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:11.724 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.738 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.744 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:11.754 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:11.754 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:11.768 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:11.768 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:11.784 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:11.784 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:11.784 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 273.35 0:00:11.784 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:11.785 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K21/simplified_contigs.fasta 0:00:11.785 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:11.785 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 11 seconds Max read length detected as 100 == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.000 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.001 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.001 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.001 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.001 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.001 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.001 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.320 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:03.871 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:03.872 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.290 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 972 kmers in total. 0:00:04.290 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.305 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.310 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.310 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.310 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.310 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:04.310 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:07.911 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 972 kmers. 0:00:08.523 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:08.894 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 973 kmers in total. 0:00:08.894 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:08.918 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.478 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.479 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.3782 bits per kmer). 0:00:09.479 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.546 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.546 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:09.546 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:09.546 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:09.602 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 5 34-mers were removed by early tip clipper 0:00:09.602 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.602 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.614 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:09.626 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:09.650 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:09.674 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:09.674 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:09.674 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.066 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.5267 bits per kmer). 0:00:10.066 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.122 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.151 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:10.151 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:10.151 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:10.151 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:10.182 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:10.182 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:10.226 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:10.226 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:10.258 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:10.258 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:10.294 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 0 times 0:00:10.294 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:10.294 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:10.294 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:10.294 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:10.294 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.330 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.330 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.354 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.354 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.378 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:10.378 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.402 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.402 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.426 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.426 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:10.450 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:10.450 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:10.450 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:10.450 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:10.450 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:10.474 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:10.474 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:10.498 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:10.498 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:10.522 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:10.522 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:10.542 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:10.542 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.566 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.566 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:10.574 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:10.574 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.590 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.590 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:10.606 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:10.606 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:10.626 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:10.627 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:10.642 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:10.642 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:10.654 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:10.654 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:10.670 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:10.670 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:10.686 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:10.686 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:10.710 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:10.710 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:10.718 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:10.718 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:10.734 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:10.734 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:10.750 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:10.750 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:10.766 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:10.766 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:10.766 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.839 0:00:10.766 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:10.766 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:10.767 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:10.767 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 10 seconds == Running assembler: K55 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K55/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K55/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K55/configs/meta_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=55 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 1 0:00:00.000 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.005 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.005 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1526 0:00:00.005 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.005 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.005 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.005 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.829 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.418 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.418 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.829 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:04.829 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.865 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.865 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.865 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.866 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.866 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:04.866 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.410 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 949 kmers. 0:00:08.937 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.285 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:09.285 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.301 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:09.777 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:09.778 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (82.1703 bits per kmer). 0:00:09.778 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:09.833 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:09.833 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:09.833 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:09.869 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 4 sequences extracted 0:00:09.913 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:09.933 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:09.977 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:09.977 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.489 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:10.489 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.513 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.546 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:10.546 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:10.546 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.546 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:10.546 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:10.546 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:10.546 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:14.325 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 8 sequences. 0:00:14.914 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:15.265 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 949 kmers in total. 0:00:15.265 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:15.290 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:15.721 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:15.722 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.2086 bits per kmer). 0:00:15.722 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:15.757 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:15.758 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:15.758 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:15.793 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:15.793 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:15.793 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:15.793 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 4 candidates 0:00:15.813 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:15.813 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:15.813 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:15.837 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:15.837 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial tip clipper 0:00:15.861 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial tip clipper triggered 0 times 0:00:15.861 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial ec remover 0:00:15.881 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial ec remover triggered 0 times 0:00:15.881 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with low flanking coverage 0:00:15.893 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with low flanking coverage triggered 0 times 0:00:15.893 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Initial isolated edge remover 0:00:15.917 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Initial isolated edge remover triggered 1 times 0:00:15.917 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Simplification 0:00:15.917 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:15.917 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:15.917 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:15.917 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.929 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:15.929 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.941 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.941 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:15.965 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:15.965 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:15.981 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:15.981 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:15.997 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:15.997 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.017 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.017 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:16.017 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:16.017 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:16.017 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:16.017 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:16.017 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:16.017 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:19.893 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:20.557 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:20.979 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:20.979 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:20.999 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:21.477 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:21.478 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:21.478 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:21.509 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:21.510 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:21.510 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:21.541 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:21.541 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:21.541 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:21.541 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:21.569 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Paired Information Counting 0:00:21.569 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:21.569 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:21.569 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:21.889 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:22.878 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:22.979 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:22.979 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:22.982 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 0:00:23.092 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:23.093 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:23.106 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:23.106 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 0:00:23.120 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:23.138 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:23.151 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Distance Estimation 0:00:23.151 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:23.151 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:23.151 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:23.157 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:23.157 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:23.157 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:23.197 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:23.241 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:23.241 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:23.241 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:23.265 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:23.265 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:23.265 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:23.265 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:23.265 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Preliminary Repeat Resolving 0:00:23.265 64M / 8G INFO General (repeat_resolving.cpp : 56) Setting up preliminary path extend settings 0:00:23.265 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:23.265 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:23.265 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:23.265 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:23.265 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 3 0:00:23.265 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:23.265 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:23.265 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:23.265 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:23.265 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:23.266 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:23.266 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:23.266 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:23.266 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:23.266 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:23.266 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:23.266 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:23.266 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:23.266 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:23.266 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:23.266 64M / 8G INFO General (repeat_resolving.cpp : 75) Restoring initial path extend settings 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:23.266 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:23.266 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Second Phase Setup 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 20) Preparing second phase 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 28) Moving preliminary contigs from /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta to /build/spades-3.13.1+dfsg/spades_test//K55/first_pe_contigs.fasta 0:00:23.266 64M / 8G INFO General (second_phase_setup.cpp : 40) Ready to run second phase 0:00:23.266 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:23.266 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:23.266 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:23.266 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:23.266 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:23.277 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:23.277 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:23.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:23.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:23.309 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:23.309 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:23.325 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:23.325 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:23.341 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:23.341 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:23.357 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:23.357 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:23.357 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:23.357 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:23.357 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:23.357 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:23.357 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:23.357 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:27.673 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:28.226 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:28.558 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 945 kmers in total. 0:00:28.558 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:28.582 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:29.053 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:29.054 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9752 bytes occupied (82.5566 bits per kmer). 0:00:29.054 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:29.093 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:29.094 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:29.094 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:29.118 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:29.118 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:29.118 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:29.118 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:29.153 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:29.153 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:29.153 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:29.153 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:29.153 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:29.169 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:29.169 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:29.193 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:29.193 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:29.205 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:29.205 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:29.229 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:29.229 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:29.245 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:29.245 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:29.261 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:29.261 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:29.285 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:29.285 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:29.297 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:29.297 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:29.321 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:29.321 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:29.337 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:29.337 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Disconnecting edges with relatively low coverage 0:00:29.353 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Disconnecting edges with relatively low coverage triggered 0 times 0:00:29.353 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex tip clipper 0:00:29.369 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex tip clipper triggered 0 times 0:00:29.369 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:29.393 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:29.393 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:29.405 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:29.405 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:29.417 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:29.417 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:29.433 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:29.433 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:29.449 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:29.449 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Thorn remover (meta) 0:00:29.465 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Thorn remover (meta) triggered 0 times 0:00:29.465 64M / 8G INFO General (simplification.cpp : 326) Running Hidden EC remover (meta) 0:00:29.485 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:29.485 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:29.501 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:29.501 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:29.501 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 140.62 0:00:29.501 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:29.501 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:29.501 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:29.525 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:29.525 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:29.525 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:29.526 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:29.526 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:29.526 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:29.526 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:29.526 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.fasta 0:00:29.526 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:29.526 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:29.526 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 900 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:29.526 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:29.808 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:30.764 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:30.867 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:30.868 336M / 8G INFO General (pair_info_count.cpp : 211) 1636 paired reads (79.6495% of all) aligned to long edges 0:00:30.871 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.696, deviation = 10.4821, left quantile = 201, right quantile = 228, read length = 100 0:00:30.979 256M / 8G INFO General (pair_info_count.cpp : 374) Filtering data for library #0 0:00:30.979 256M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:30.993 256M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:30.993 256M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 1, rounding threshold 0 0:00:31.029 268M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:31.061 268M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:31.095 64M / 8G INFO General (pair_info_count.cpp : 330) Mapping contigs library #1 0:00:31.095 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:31.096 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 1 reads processed 0:00:31.096 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:31.096 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:31.096 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:31.096 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:31.117 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:31.117 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:31.117 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:31.141 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:31.177 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:31.177 64M / 8G INFO General (distance_estimation.cpp : 103) Filling scaffolding index 0:00:31.177 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SMOOTHING distance estimator 0:00:31.201 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:31.201 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:31.201 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:31.201 64M / 8G INFO General (distance_estimation.cpp : 182) Clearing raw paired index 0:00:31.201 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:31.201 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:31.201 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:31.201 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 34) resolvable_repeat_length_bound set to 10000 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 477) Using 1 single read library 0:00:31.201 64M / 8G INFO General (launcher.cpp : 359) Filling backbone edges for long reads scaffolding... 0:00:31.201 64M / 8G INFO General (launcher.cpp : 361) with long reads paths 0:00:31.201 64M / 8G INFO General (launcher.cpp : 370) Removing fake unique with paired-end libs 0:00:31.201 64M / 8G INFO General (launcher.cpp : 381) 0 unique edges 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 389) Using 0 long reads scaffolding libraries 0:00:31.201 64M / 8G INFO General (extenders_logic.cpp : 399) Using additional coordinated coverage extender 0:00:31.201 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 0:00:31.202 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:31.202 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:31.202 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:31.202 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:31.202 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:31.202 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:31.202 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:31.202 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:31.202 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:31.202 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:31.202 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 295) Removing overlaps 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 305) Marking overlaps 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 130) Marking start/end overlaps 0:00:31.202 64M / 8G INFO OverlapRemover (pe_resolver.hpp : 133) Marking remaining overlaps 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 308) Splitting paths 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 313) Deduplicating paths 0:00:31.202 64M / 8G INFO PEResolver (pe_resolver.hpp : 315) Overlaps removed 0:00:31.202 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:31.202 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:31.202 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph_with_scaffolds.gfa 0:00:31.202 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K55/before_rr.fasta 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K55/assembly_graph.fastg 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/final_contigs.paths 0:00:31.202 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K55/scaffolds.paths 0:00:31.202 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:31.203 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 31 seconds ===== Assembling finished. Used k-mer sizes: 21, 33, 55 * Corrected reads are in /build/spades-3.13.1+dfsg/spades_test/corrected/ * Assembled contigs are in /build/spades-3.13.1+dfsg/spades_test/contigs.fasta * Assembled scaffolds are in /build/spades-3.13.1+dfsg/spades_test/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /build/spades-3.13.1+dfsg/spades_test/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /build/spades-3.13.1+dfsg/spades_test/scaffolds.paths * Assembly graph is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log Thank you for using SPAdes! /build/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py --test Command line: /build/spades-3.13.1+dfsg/install_spades/bin/rnaspades.py --test System information: SPAdes version: 3.13.1 Python version: 3.9.2 OS: Linux-5.14.0-0.bpo.2-amd64-x86_64-with-glibc2.31 Output dir: /build/spades-3.13.1+dfsg/spades_test Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: RNA-seq mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/build/share/spades/test_dataset/ecoli_1K_1.fq.gz'] right reads: ['/build/share/spades/test_dataset/ecoli_1K_2.fq.gz'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: automatic selection based on read length Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /build/spades-3.13.1+dfsg/spades_test/tmp Threads: 16 Memory limit (in Gb): 47 ======= SPAdes pipeline started. Log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log /build/share/spades/test_dataset/ecoli_1K_1.fq.gz: max reads length: 100 /build/share/spades/test_dataset/ecoli_1K_2.fq.gz: max reads length: 100 Reads length: 100 K values to be used: [33, 49] ===== Assembling started. == Running assembler: K33 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K33/configs/rna_mode.info 0:00:00.000 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.000 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.000 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=33 0:00:00.000 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.000 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.000 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.000 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 77) Converting reads to binary format for library #0 (takes a while) 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 78) Converting paired reads 0:00:00.125 68M / 72M INFO General (binary_converter.hpp : 117) 2054 reads written 0:00:00.126 4M / 72M INFO General (read_converter.hpp : 87) Converting single reads 0:00:00.313 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.314 4M / 140M INFO General (read_converter.hpp : 95) Converting merged reads 0:00:00.523 132M / 140M INFO General (binary_converter.hpp : 117) 0 reads written 0:00:00.525 4M / 140M INFO General (construction.cpp : 111) Max read length 100 0:00:00.525 4M / 140M INFO General (construction.cpp : 117) Average read length 86.1611 0:00:00.525 4M / 140M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.525 4M / 140M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.527 4M / 140M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.527 4M / 140M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.527 4M / 140M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:04.473 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:05.016 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:05.016 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:05.450 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 974 kmers in total. 0:00:05.451 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:05.474 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:05.483 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:05.483 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:05.483 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:05.483 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:05.483 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:09.075 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 974 kmers. 0:00:09.615 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.986 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 975 kmers in total. 0:00:09.987 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:10.010 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.450 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.451 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9776 bytes occupied (80.2133 bits per kmer). 0:00:10.451 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.522 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.523 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Early tip clipping 0:00:10.523 64M / 8G INFO General (construction.cpp : 253) Early tip clipper length bound set as (RL - K) 0:00:10.523 64M / 8G INFO Early tip clipping (early_simplification.hpp : 181) Early tip clipping 0:00:10.595 64M / 8G INFO Early tip clipping (early_simplification.hpp : 184) 7 34-mers were removed by early tip clipper 0:00:10.595 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.595 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.622 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 1 sequences extracted 0:00:10.658 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.695 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.731 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.731 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.731 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:11.107 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9784 bytes occupied (80.3614 bits per kmer). 0:00:11.107 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:11.186 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:11.228 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:11.228 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 72 0:00:11.228 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 225.865 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 22.5865 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 22.5865 0:00:11.228 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:11.228 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:11.228 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:11.228 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:11.228 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:11.259 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:11.259 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:00:11.259 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT 0:00:11.318 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times 0:00:11.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:00:11.359 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:00:11.359 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:11.387 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:11.387 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections 0:00:11.387 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 0:00:11.387 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:11.387 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:11.387 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:11.387 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:11.387 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.387 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:11.387 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.419 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.419 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.451 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.451 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.463 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.463 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.487 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.487 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:11.487 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.499 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.499 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.510 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.511 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.535 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.535 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.559 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.559 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.559 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:11.559 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.570 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.571 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.595 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.595 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.623 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.623 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.651 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.651 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:11.651 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.663 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.663 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.687 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.687 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.699 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.735 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.735 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.735 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:11.735 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.742 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.743 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.767 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.767 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.778 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.779 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.791 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.791 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.791 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:11.791 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.807 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.807 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.822 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.823 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.847 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.847 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.859 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.859 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.859 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:11.859 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.871 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.871 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.887 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.887 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.903 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.903 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.927 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.927 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.927 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:11.927 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:11.938 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:11.939 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:11.951 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:11.951 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:11.967 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:11.967 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:11.983 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:11.984 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:11.984 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:11.984 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.006 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.007 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.019 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.019 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.031 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.031 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.047 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.047 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.047 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:12.047 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.063 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.063 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.079 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.079 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.103 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.103 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.111 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.111 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.111 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:12.111 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.127 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.127 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:12.143 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:12.143 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.159 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.159 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:12.183 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:12.183 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:12.183 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:12.183 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:12.183 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:12.183 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:12.190 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:12.190 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:12.207 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:12.207 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:12.223 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:12.223 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.247 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.247 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:12.259 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:12.259 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.283 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.283 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:12.295 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:12.295 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:12.319 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:12.319 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:12.330 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:12.331 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:12.343 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:12.343 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:12.359 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:12.359 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:12.375 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:12.375 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:12.399 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:12.399 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:12.411 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:12.411 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:12.423 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:12.423 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:12.439 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:12.439 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:12.439 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:12.455 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:12.455 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:12.455 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 225.865 0:00:12.455 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:12.455 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K33/simplified_contigs.fasta 0:00:12.455 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:12.455 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 12 seconds Max read length detected as 100 == Running assembler: K49 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/config.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/mda_mode.info 0:00:00.000 4M / 4M INFO General (main.cpp : 74) Loaded config from /build/spades-3.13.1+dfsg/spades_test/K49/configs/rna_mode.info 0:00:00.001 4M / 4M INFO General (memory_limit.cpp : 49) Memory limit set to 47 Gb 0:00:00.001 4M / 4M INFO General (main.cpp : 84) Starting SPAdes, built from N/A, git revision N/A 0:00:00.001 4M / 4M INFO General (main.cpp : 88) Maximum k-mer length: 128 0:00:00.001 4M / 4M INFO General (main.cpp : 89) Assembling dataset (/build/spades-3.13.1+dfsg/spades_test/dataset.info) with K=49 0:00:00.001 4M / 4M INFO General (main.cpp : 90) Maximum # of threads to use (adjusted due to OMP capabilities): 16 0:00:00.001 4M / 4M INFO General (launch.hpp : 52) SPAdes started 0:00:00.001 4M / 4M INFO General (launch.hpp : 59) Starting from stage: construction 0:00:00.001 4M / 4M INFO General (launch.hpp : 66) Two-step RR enabled: 0 0:00:00.001 4M / 4M INFO General (launch.hpp : 77) Will need read mapping, kmer mapper will be attached 0:00:00.001 4M / 4M INFO StageManager (stage.cpp : 132) STAGE == de Bruijn graph construction 0:00:00.001 4M / 4M INFO General (read_converter.hpp : 59) Binary reads detected 0:00:00.002 4M / 4M INFO General (construction.cpp : 111) Max read length 100 0:00:00.002 4M / 4M INFO General (construction.cpp : 117) Average read length 86.1611 0:00:00.002 4M / 4M INFO General (stage.cpp : 101) PROCEDURE == k+1-mer counting 0:00:00.002 4M / 4M INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:00.002 4M / 4M INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.979085 Gb 0:00:00.002 4M / 4M INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:03.680 8G / 8G INFO General (kmer_splitters.hpp : 295) Adding contigs from previous K 0:00:04.222 64M / 8G INFO General (kmer_splitters.hpp : 308) Used 8216 reads 0:00:04.222 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:04.648 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. 0:00:04.648 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:04.685 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Extension index construction 0:00:04.685 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:04.685 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:04.685 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:04.685 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:04.685 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:08.828 8G / 8G INFO General (kmer_splitters.hpp : 385) Used 958 kmers. 0:00:09.363 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:09.764 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 959 kmers in total. 0:00:09.764 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:09.800 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.296 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:10.297 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9768 bytes occupied (81.4849 bits per kmer). 0:00:10.297 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 99) Building k-mer extensions from k+1-mers 0:00:10.372 64M / 8G INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 103) Building k-mer extensions from k+1-mers finished. 0:00:10.372 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Condensing graph 0:00:10.372 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 355) Extracting unbranching paths 0:00:10.404 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 374) Extracting unbranching paths finished. 5 sequences extracted 0:00:10.416 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 310) Collecting perfect loops 0:00:10.436 64M / 8G INFO UnbranchingPathExtractor (debruijn_graph_constructor: 343) Collecting perfect loops finished. 0 loops collected 0:00:10.484 64M / 8G INFO General (stage.cpp : 101) PROCEDURE == Filling coverage indices (PHM) 0:00:10.484 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.484 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:10.900 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). 0:00:10.900 64M / 8G INFO General (construction.cpp : 388) Collecting k-mer coverage information from reads, this takes a while. 0:00:10.948 64M / 8G INFO General (construction.cpp : 508) Filling coverage and flanking coverage from PHM 0:00:10.984 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == EC Threshold Finding 0:00:10.984 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 114) Bucket size: 53 0:00:10.984 64M / 8G INFO ThresholdFinder (ec_threshold_finder.hpp : 129) Proper threshold was not found. Threshold set to 0.1 of average coverage 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 98) Average edge coverage: 162.219 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 99) Graph threshold: 16.2219 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 127) EC coverage threshold value was calculated as 16.2219 0:00:10.984 64M / 8G INFO General (genomic_info_filler.cpp : 128) Trusted kmer low bound: 0 0:00:10.984 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:10.984 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:10.985 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:10.985 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:10.985 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:10.985 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:10.985 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:14.976 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 10 sequences. 0:00:15.535 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:15.916 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 958 kmers in total. 0:00:15.916 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:15.946 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:16.336 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:16.337 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (81.5031 bits per kmer). 0:00:16.337 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:16.388 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:16.388 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:16.388 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:16.424 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:16.424 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:16.424 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:16.424 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:16.456 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Raw Simplification 0:00:16.456 64M / 8G INFO General (simplification.cpp : 128) PROCEDURE == InitialCleaning 0:00:16.456 64M / 8G INFO General (graph_simplification.hpp : 669) Flanking coverage based disconnection disabled 0:00:16.456 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Self conjugate edge remover 0:00:16.492 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Self conjugate edge remover triggered 0 times 0:00:16.492 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Remover of short poly-AT edges 0:00:16.492 64M / 8G INFO General (simplification.cpp : 76) Removing short polyAT 0:00:16.544 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Remover of short poly-AT edges triggered 0 times 0:00:16.544 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Short PolyA/T Edges 0:00:16.572 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Short PolyA/T Edges triggered 0 times 0:00:16.572 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:16.596 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 1 times 0:00:16.596 64M / 8G INFO General (graph_simplification.hpp : 708) Removing loops and rc loops with erroneous connections 0:00:16.596 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 408) Loops: accurately removed/deadend removed/other: 0/0/0 0:00:16.596 64M / 8G INFO ECLoopRemover (erroneous_connection_remov: 409) RC loops: accurately removed/deadend removed/other: 0/0/0 0:00:16.596 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification 0:00:16.596 64M / 8G INFO General (simplification.cpp : 357) Graph simplification started 0:00:16.596 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:16.596 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:16.596 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 1 0:00:16.596 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.612 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 1 times 0:00:16.612 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.640 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.640 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.664 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.687 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:16.687 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.687 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 2 0:00:16.687 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.708 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.708 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.732 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.732 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.760 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.760 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.780 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:16.780 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.780 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 3 0:00:16.780 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.804 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.804 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.828 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.828 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.852 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.852 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.876 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.876 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 4 0:00:16.876 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.896 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.896 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.912 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.912 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.928 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:16.944 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:16.944 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:16.944 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 5 0:00:16.944 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:16.960 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:16.960 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:16.976 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:16.976 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:16.992 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:16.992 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.008 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.008 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.008 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 6 0:00:17.008 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.024 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.024 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.040 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.040 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.056 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.056 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.072 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.072 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.072 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 7 0:00:17.072 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.088 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.088 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.104 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.104 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.120 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.120 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.136 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.136 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.136 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 8 0:00:17.136 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.156 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.156 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.172 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.172 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.188 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.188 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.204 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.204 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.204 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 9 0:00:17.204 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.228 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.228 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.240 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.240 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.264 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.264 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.276 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.276 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.276 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 10 0:00:17.276 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.288 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.288 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.304 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.304 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.320 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.320 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.336 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.336 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.336 64M / 8G INFO General (simplification.cpp : 362) PROCEDURE == Simplification cycle, iteration 11 0:00:17.336 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:17.356 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:17.356 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Dead end clipper 0:00:17.368 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Dead end clipper triggered 0 times 0:00:17.368 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:17.384 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:17.384 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Low coverage edge remover 0:00:17.400 64M / 8G INFO ConditionParser (graph_simplification.hpp : 188) Creating relative coverage EC condition with threshold 1 0:00:17.400 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Low coverage edge remover triggered 0 times 0:00:17.400 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Gap Closer 0:00:17.400 64M / 8G INFO General (graph_pack.hpp : 101) Index refill 0:00:17.400 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 301) Building kmer index 0:00:17.400 64M / 8G INFO General (kmer_index_builder.hpp : 117) Splitting kmer instances into 256 files using 16 threads. This might take a while. 0:00:17.400 64M / 8G INFO General (file_limit.hpp : 32) Open file limit set to 1024 0:00:17.400 64M / 8G INFO General (kmer_splitters.hpp : 89) Memory available for splitting buffers: 0.977865 Gb 0:00:17.400 64M / 8G INFO General (kmer_splitters.hpp : 97) Using cell size of 131072 0:00:21.000 8G / 8G INFO General (edge_index_builders.hpp : 82) Used 2 sequences. 0:00:21.566 64M / 8G INFO General (kmer_index_builder.hpp : 120) Starting k-mer counting. 0:00:21.944 64M / 8G INFO General (kmer_index_builder.hpp : 127) K-mer counting done. There are 951 kmers in total. 0:00:21.944 64M / 8G INFO General (kmer_index_builder.hpp : 133) Merging temporary buckets. 0:00:21.983 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 314) Building perfect hash indices 0:00:22.384 64M / 8G INFO General (kmer_index_builder.hpp : 150) Merging final buckets. 0:00:22.385 64M / 8G INFO K-mer Index Building (kmer_index_builder.hpp : 336) Index built. Total 9760 bytes occupied (82.103 bits per kmer). 0:00:22.385 64M / 8G INFO General (edge_index_builders.hpp : 107) Collecting edge information from graph, this takes a while. 0:00:22.436 64M / 8G INFO General (edge_index.hpp : 92) Index refilled 0:00:22.436 64M / 8G INFO General (gap_closer.cpp : 159) Preparing shift maps 0:00:22.436 64M / 8G INFO General (gap_closer.cpp : 119) Processing paired reads (takes a while) 0:00:22.464 64M / 8G INFO General (gap_closer.cpp : 138) Used 2054 paired reads 0:00:22.464 64M / 8G INFO General (gap_closer.cpp : 140) Merging paired indices 0:00:22.464 64M / 8G INFO GapCloser (gap_closer.cpp : 346) Closing short gaps 0:00:22.464 64M / 8G INFO GapCloser (gap_closer.cpp : 378) Closing short gaps complete: filled 0 gaps after checking 0 candidates 0:00:22.496 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Simplification Cleanup 0:00:22.496 64M / 8G INFO General (simplification.cpp : 196) PROCEDURE == Post simplification 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 458) Disconnection of relatively low covered edges disabled 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 494) Complex tip clipping disabled 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:22.496 64M / 8G INFO General (graph_simplification.hpp : 641) Creating parallel br instance 0:00:22.496 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:22.524 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:22.524 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:22.548 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:22.548 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:22.572 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:22.572 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:22.592 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:22.592 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:22.624 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:22.624 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:22.644 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:22.644 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:22.668 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:22.668 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:22.688 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:22.688 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage EC remover 0:00:22.720 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage EC remover triggered 0 times 0:00:22.720 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Relative coverage component remover 0:00:22.744 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Relative coverage component remover triggered 0 times 0:00:22.744 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Complex bulge remover 0:00:22.768 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Complex bulge remover triggered 0 times 0:00:22.768 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Tip clipper 0:00:22.792 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Tip clipper triggered 0 times 0:00:22.792 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final tip clipper 0:00:22.816 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final tip clipper triggered 0 times 0:00:22.816 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Bulge remover 0:00:22.840 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Bulge remover triggered 0 times 0:00:22.840 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Final bulge remover 0:00:22.864 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Final bulge remover triggered 0 times 0:00:22.864 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running AT Tips 0:00:22.880 64M / 8G INFO Simplification (parallel_processing.hpp : 167) AT Tips triggered 0 times 0:00:22.880 64M / 8G INFO General (simplification.cpp : 330) Disrupting self-conjugate edges 0:00:22.880 64M / 8G INFO Simplification (parallel_processing.hpp : 165) Running Removing isolated edges 0:00:22.912 64M / 8G INFO Simplification (parallel_processing.hpp : 167) Removing isolated edges triggered 0 times 0:00:22.912 64M / 8G INFO General (simplification.cpp : 470) Counting average coverage 0:00:22.912 64M / 8G INFO General (simplification.cpp : 476) Average coverage = 163.37 0:00:22.912 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Mismatch Correction 0:00:22.912 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:22.912 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:22.930 64M / 8G INFO General (mismatch_shall_not_pass.hp: 189) Finished collecting potential mismatches positions 0:00:22.930 64M / 8G INFO General (mismatch_shall_not_pass.hp: 290) All edges processed 0:00:22.930 64M / 8G INFO General (mismatch_correction.cpp : 27) Corrected 0 nucleotides 0:00:22.930 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:22.930 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa 0:00:22.930 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta 0:00:22.930 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg 0:00:22.931 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/final_contigs.fasta 0:00:22.931 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Paired Information Counting 0:00:22.931 64M / 8G INFO General (graph_pack.hpp : 109) Normalizing k-mer map. Total 0 kmers to process 0:00:22.931 64M / 8G INFO General (graph_pack.hpp : 111) Normalizing done 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 323) Min edge length for estimation: 951 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 334) Estimating insert size for library #0 0:00:22.931 64M / 8G INFO General (pair_info_count.cpp : 190) Estimating insert size (takes a while) 0:00:23.108 336M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:23.922 336M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:24.023 336M / 8G INFO General (pair_info_count.cpp : 209) Edge pairs: 67108864 (rough upper limit) 0:00:24.023 336M / 8G INFO General (pair_info_count.cpp : 211) 1751 paired reads (85.2483% of all) aligned to long edges 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 353) Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 386) Mapping library #0 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 388) Mapping paired reads (takes a while) 0:00:24.026 64M / 8G INFO General (pair_info_count.cpp : 286) Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0 0:00:24.040 76M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:24.060 76M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 2054 reads processed 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 395) Mapping single reads of library #0 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 255) Will calculate lib coverage as well 0:00:24.090 64M / 8G INFO General (pair_info_count.cpp : 39) Selecting usual mapper 0:00:24.116 64M / 8G INFO General (sequence_mapper_notifier.h: 98) Total 4108 reads processed 0:00:24.116 64M / 8G INFO General (pair_info_count.cpp : 397) Total paths obtained from single reads: 0 0:00:24.116 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Distance Estimation 0:00:24.116 64M / 8G INFO General (distance_estimation.cpp : 173) Processing library #0 0:00:24.116 64M / 8G INFO General (distance_estimation.cpp : 149) Weight Filter Done 0:00:24.116 64M / 8G INFO DistanceEstimator (distance_estimation.hpp : 116) Using SIMPLE distance estimator 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 34) Filtering info 0:00:24.128 64M / 8G INFO General (pair_info_filters.hpp : 242) Start filtering; index size: 2 0:00:24.128 64M / 8G INFO General (pair_info_filters.hpp : 263) Done filtering 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 156) Refining clustered pair information 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 158) The refining of clustered pair information has been finished 0:00:24.128 64M / 8G INFO General (distance_estimation.cpp : 160) Improving paired information 0:00:24.176 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:24.212 64M / 8G INFO PairInfoImprover (pair_info_improver.hpp : 102) Paired info stats: missing = 0; contradictional = 0 0:00:24.212 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Repeat Resolving 0:00:24.212 64M / 8G INFO General (repeat_resolving.cpp : 69) Using Path-Extend repeat resolving 0:00:24.212 64M / 8G INFO General (launcher.cpp : 481) ExSPAnder repeat resolving tool started 0:00:24.212 64M / 8G INFO General (launcher.cpp : 392) Creating main extenders, unique edge length = 2000 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 475) Using 1 paired-end library 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 476) Using 1 paired-end scaffolding library 0:00:24.212 64M / 8G INFO General (extenders_logic.cpp : 477) Using 0 single read libraries 0:00:24.212 64M / 8G INFO General (launcher.cpp : 420) Total number of extenders is 5 0:00:24.212 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:24.212 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:24.212 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:24.212 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:24.212 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:24.212 64M / 8G INFO General (launcher.cpp : 427) Closing gaps in paths 0:00:24.212 64M / 8G INFO General (launcher.cpp : 455) Gap closing completed 0:00:24.212 64M / 8G INFO General (launcher.cpp : 286) Traversing tandem repeats 0:00:24.212 64M / 8G INFO General (launcher.cpp : 296) Traversed 0 loops 0:00:24.212 64M / 8G INFO General (launcher.cpp : 234) Finalizing paths 0:00:24.212 64M / 8G INFO General (launcher.cpp : 236) Deduplicating paths 0:00:24.212 64M / 8G INFO General (launcher.cpp : 240) Paths deduplicated 0:00:24.212 64M / 8G INFO General (launcher.cpp : 247) Overlaps will not be removed 0:00:24.212 64M / 8G INFO General (launcher.cpp : 257) Paths finalized 0:00:24.212 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - hard 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 2 converted to 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 180 bp converted to 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 151 0:00:24.212 64M / 8G INFO General (launcher.cpp : 466) Finalizing paths - soft 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.05 converted to 56 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 85 bp converted to 56 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 56 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:24.212 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.2 converted to 71 0:00:24.212 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 100 bp converted to 71 0:00:24.212 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 71 0:00:24.213 64M / 8G INFO General (launcher.cpp : 474) Finalizing main paths 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.3 converted to 81 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 110 bp converted to 81 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 81 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.6 converted to 111 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 140 bp converted to 111 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 111 0:00:24.213 64M / 8G INFO General (launcher.cpp : 279) Read length relative cutoff 1.5 converted to 101 0:00:24.213 64M / 8G INFO General (launcher.cpp : 280) Read length absolute cutoff 130 bp converted to 101 0:00:24.213 64M / 8G INFO General (launcher.cpp : 281) Length cutoff: 101 0:00:24.213 64M / 8G INFO General (launcher.cpp : 534) ExSPAnder repeat resolving tool finished 0:00:24.213 64M / 8G INFO StageManager (stage.cpp : 132) STAGE == Contig Output 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 45) Writing GFA to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph_with_scaffolds.gfa 0:00:24.213 64M / 8G INFO General (contig_output.hpp : 22) Outputting contigs to /build/spades-3.13.1+dfsg/spades_test//K49/before_rr.fasta 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 56) Outputting FastG graph to /build/spades-3.13.1+dfsg/spades_test//K49/assembly_graph.fastg 0:00:24.213 64M / 8G INFO General (contig_output_stage.cpp : 20) Outputting FastG paths to /build/spades-3.13.1+dfsg/spades_test//K49/transcripts.paths 0:00:24.213 64M / 8G INFO General (launch.hpp : 151) SPAdes finished 0:00:24.213 64M / 8G INFO General (main.cpp : 109) Assembling time: 0 hours 0 minutes 24 seconds ===== Assembling finished. Used k-mer sizes: 33, 49 * Assembled transcripts are in /build/spades-3.13.1+dfsg/spades_test/transcripts.fasta * Paths in the assembly graph corresponding to the transcripts are in /build/spades-3.13.1+dfsg/spades_test/transcripts.paths * Hard filtered transcripts are in /build/spades-3.13.1+dfsg/spades_test/hard_filtered_transcripts.fasta * Soft filtered transcripts are in /build/spades-3.13.1+dfsg/spades_test/soft_filtered_transcripts.fasta * Assembly graph is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph.fastg * Assembly graph in GFA format is in /build/spades-3.13.1+dfsg/spades_test/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. ========= TEST PASSED CORRECTLY. SPAdes log can be found here: /build/spades-3.13.1+dfsg/spades_test/spades.log Thank you for using SPAdes! # Difficult to test truSPAdes before installing because bwa-spades # is still not in the right place. Let's do this later in an # autopkgtest. # /build/spades-3.13.1+dfsg/install_spades/bin/truspades.py --test # Cleunup symlinks rm -rf /build/spades-3.13.1+dfsg/../share/ unlink /build/spades-3.13.1+dfsg/install_spades/bin/spades-bwa make[1]: Leaving directory '/build/spades-3.13.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --sourcedirectory=assembler/src --buildsystem=cmake dh_testroot -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_auto_install make[1]: Entering directory '/build/spades-3.13.1+dfsg' echo "Nothing to install" Nothing to install find /build/spades-3.13.1+dfsg -name *.pyc -delete make[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/spades-3.13.1+dfsg' dh_install mkdir -p debian/spades/usr/lib/spades mv debian/spades/usr/bin debian/spades/usr/lib/spades mkdir -p debian/spades/usr/bin install debian/bin/spades debian/spades/usr/bin/ chmod +x debian/spades/usr/bin/spades 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 ln -s ../../../share/spades/VERSION debian/spades/usr/lib/spades/bin/VERSION make[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules override_dh_installdocs make[1]: Entering directory '/build/spades-3.13.1+dfsg' dh_installdocs rm -f debian/spades/usr/share/spades/*.html rm -f debian/spades/usr/share/spades/manual.md make[1]: Leaving directory '/build/spades-3.13.1+dfsg' debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/spades-3.13.1+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/spades-3.13.1+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/spades-3.13.1+dfsg' mkdir -p /build/spades-3.13.1+dfsg/debian/man asciidoctor -a docdate='' -b manpage /build/spades-3.13.1+dfsg/debian/man_src/*.adoc cp /build/spades-3.13.1+dfsg/debian/man_src/*.? /build/spades-3.13.1+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/build/spades-3.13.1+dfsg' dh_python3 -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_installinit -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_link: warning: skipping link from usr/bin/spades to self 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 -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_strip -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_makeshlibs -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_shlibdeps -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_3.13.1+dfsg-2_amd64.deb'. dpkg-deb: building package 'spades' in '../spades_3.13.1+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../spades_3.13.1+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1777496 and its subdirectories I: Current time: Sat Feb 11 20:11:15 -12 2023 I: pbuilder-time-stamp: 1676189475